Munich to Berchtesgaden Logistics-Train, Bus or Car

All three of your destinations are easily reachable by train, without the hassle of refueling, parking and turning in a car. And it's less stressful for both of you. Trains are easy. Berchtesgaden is very near Salzburg, and can be reached by bus or train in I think about 15 minutes. The Deustche Bahn website bahn.com has an English option. You just put in departure station and destination and it figures out all the options for you. It's not like airlines where you have to book everything in advance, and b boarding is just getting on, like a city bus. Someone else may chime in with guidance on the different discount options. This site has a lot of good info on how the train systems work: man in seat 61

Salzburg is 27 min by car from Bechtesgaden, and an hour 15 min by train according to Google Maps. There is a beautiful lake and impressive gorges to see as well.
Use the Rome2Rio app for good guidance on train, driving, route possibilities. Personally I love driving in the Alps and a car enables me to stay anywhere, not just the center of town.
As for one scenario you mention., check to see if it is possible to return a car in Bechtesgaden-because returning it in Austria may well incur an unpleasant fee. There is also a bus from Bechtesgaden to Salzburg according to Rome2Rio app.

I would do this with public transportation all the way. Take the train from Munich to Salzburg. Use a regional train (RE5). They leave hourly at 55 minutes past from the main train station (Hbf); the trip takes 2½ hours. You will have a 6 minute change of trains in Freilassing, but it is cross-platform (2 - 3), no sweat. Purchase a Bayern-Ticket at the Hbf for 42€ (for two people). It will cover the trains from Munich to Berchtesgaden. The Hbf in Berchtesgaden is down the hill, below the town, but there are buses from the station up to town, if that is where you are staying, and the buses that day will be covered by the Bayern-Ticket too.

To get to Salzburg, take a bus, the Watzmann Express (RVO 840) from the bus plaza in front of the Hbf. The trip takes about 50 minutes and the bus goes to the Salzburg Hbf but stops a several places in the old town first. Or, take the train back through Freilassing to Salzburg Hbf.

I've been to Berchtesgaden three times (twice from Munich), and been on both the train from Freilassing and the Watzmann Express bus. If you decide to use public transportation, and once you know where you will be staying in Munich and Berchtesgaden and at what time you want to travel, I can give you more specific information.

What do you plan to do in Berchtesgaden? Most of the sights and activities theere will necessitate additional public transportation during the 48 hours you will spend there.

I would ask the same question about Munich, to be honest, which is not a place you can expect to cover on foot and imposes similar demands.

I am very comfortable with public transport in Germany. That's all I do there. But that comfort comes with years of experience, and if you are intimidated by trains, buses, etc., it would be wise to stay somewhere you can get along well without them - and to minimize the transportation you might need to short-circuit the learning curve.

Best of luck with Munich. At least Munich is a place with lots of day-tour options you could sign up for.

My suggestion for your 48 hours after Munich: keep it simple and take just ONE DIRECT TRAIN RIDE straight to Salzburg for 2 nights there.

Salzburg is not tiny but is very walkable. Your My Way tour has only one full day there (6/3.) Many Salzburg fans say Salzburg requires 2-days, 3 days if you can. So spend the night of 5/31 there, then a full day in town on 6/1 . For 6/2, you could sign up for a day tour of your choice, perhaps to Berchtesgaden, or Werfen, or...? There are lots of day tour options from Salzburg that will get you to places nearby and include specific activities/sights that would otherwise require buses or taxis:

https://www.tripadvisor.com/Attractions-g190441-Activities-c63-zfq187299-Salzburg_Austrian_Alps.html

I have arranged to stay in Berchtesgaden for two nights. Prior to that we will be in Munich. I need to know if I should buy my train ticket now or take a chance that seats will be available. I’m presuming I should book a ticket from Munich to Berchtesgaden, rather than Munich to Salzburg, followed by a bus to Berchtesgaden the same day. Thanks for all your input.

Munich Hbf > Berchtesgaden, by train only:

Your tour begins June 2, you say. So that means you plan to be in Salzburg on Sunday, June 1 at 5 pm, correct? If so, then this is a FRIDAY, May 30 morning trip.

Your trip requires 2 trains.
1, Munich > Freilassing
2, Freilassing > Berchtesgaden

• Booking seat reservations is not possible here... Seat reservations are only for long-distance trains, but these are both regional trains.

• Regional train trips are most economical with the Bayern Ticket day pass This pass is valid for both train rides at any time of day you wish. One pass that covers two-persons is priced at €42.

• Buy the ticket on Friday morning from a ticket machine. Or online. Or using the app.

• There is no need to buy in advance because it does not "sell out" - it will be available that morning. Regional train tickets like this one are not connected to a seat. It's like buying a ticket for a municipal bus back home. You buy the ticket, then you get on and look for a seat. To ensure your choice of seats, arrive early at the Munich station platform where your train departs.

• There are no refunds for the Bayern Ticket. If you buy it on the day before, be sure to buy it for the CORRECT DATE of travel.

https://int.bahn.de/en/offers/regional/regional-day-ticket-bavaria

• On Friday, the Bayern Ticket is valid only after 9 am. The trip will take about 2.5 hours. Possible trips on your date of May 30:

Train 1: Munich > Freilassing
This train will stop in Freilassing on its way to Salzburg, the train's end-destination.
(At the station, check the big departure board to see which track number to walk to for the trip to Salzburg, as it may not leave from the same track promised at the online schedule.)

Leave Munich Hbf at 9:55, 10:55, or 11:55
Arrive Freilassing on track #2 at 11:33, 12:33, or 13:33

Train 2: Freilassing > Berchtesgaden
Once the train stops in Freilassing, you will have 6 minutes to get off and to board your next train, which should be waiting for you on track #3, just across the platform. This train leaves at :39 after the hour and arrives in Berchtesgaden at :28 after the next hour.

For the trip to Salzburg on June 1, it's the same idea if you want to use only the trains. Use the Bayern Ticket. It's a Sunday, so it's valid before 9 am if you wish to travel early. Ride the regional train to Freilassing. Then ride any regional train to Salzburg.

NOTE: To find these regional train trips online, click on "mode of transport" and deselect the buses. That way, you won't see any bus journeys and won't be looking at any schedules for the long-distance trains that connect with the buses (the trains which are no good on the Bayern Ticket.)

I definitely agree with your decision to spend two nights in Berchtesgaden. I spent one day in Salzburg and saw everything I wanted to see. I've spent 15 nights in Berchtesgaden on four trips and still might go back some day. But to be perfectly honest, I prefer smaller towns, scenic areas, etc. Anyway, the first day of you tour will be in Salzburg, so you will have time to see it.

I thought Russ gave excellent instruction on how to get to Berchtesgaden via Freilassing. I do want to add that the train change in Freilassing is very fast and simple. The train to Berchtesgaden should be waiting on the opposite side of the platform. If you go into Salzburg Hbf and take the bus (RVO 840) to Berchtesgaden, you have to go outside the station, and the bus stop is not right there in the plaza. It's on a side street, Karl-Wurmb-Strasse, off the north side of the plaza. There is a much greater chance of getting lost making the change in Salzburg than in Freilassing.

Also, I don't think the Bayern-Ticket covers the section of the bus trip from Salzburg Hbf to the Austrian/German border at Hangendenstein. You'd need a separate ticket for that section. At least, as I read the rules, it doesn't. I have seen other claim that it did for them, but I think the bus driver just "cut them a break". If you purchase a single trip ticket specifically for Berchtesgaden to Salzburg (or V-V) or an RVO Tagesticket, then your travel on an RVO bus outside of Germany would be included.

Finally, for the trip to Salzburg the last morning, I'd take the bus. You catch the bus to Salzburg at a bus stop in front of the train station, and the bus comes into Salzburg from the south-east, and makes about six stops in the old town on the way to the Hbf. If, as I suspect, your hotel will be in the old town, taking the bus will prevent back tracking from the Hbf, where the train from Freilassing arrives.

I know that a Tagesticket (day ticket) for the RVO is €13,65 per person, a little less than half of a €42 Bayern-Ticket, and, as I said, it stops in the old town on the way to the Hbf. A single trip ticket from Berchtesgaden to Salzburg might be less (it was when I took the trip in 2012).

Sorry, it slipped my mind to mention that your train trip from Berchtesgaden to Salzburg will not require purchase of a ticket:

You can also travel for free on the Bavarian Regiobahn (BRB) by
presenting your Guest Card in the Berchtesgaden region, including all
the way to Bad Reichenhall and Salzburg.

The guest card is offered to all guests in Berchtesgaden. The quoted line above and further details can be found here:

https://www.berchtesgaden.de/en/general-information/guest-card

Also, I don't think the Bayern-Ticket covers the section of the bus trip from Salzburg Hbf to the Austrian/German border

Quoting https://albus.at/de/linie-840-watzmannexpress-2020/ (the site of the Austrian partner of the Watzmann Express):

"Bayern-Tickets are recognized on line 840 [...]. Bayern-Tickets can also be purchased directly from the bus driver."

The situation is different with the Deutschland-Ticket, which is actually only valid on the Bavarian side of the border and not in Salzburg.

Please get to the Königssee and further on to St Bartholomä on a boat weather permitting. It’s beautiful and the best thing you can do there.
https://www.foto-webcam.eu/webcam/funtenseetauern/