flying to munich in august for 9 days

I assume that actually means 9 nights. It is a bit tight for 9 nights and hit all your spots.
Day 1 Munich
Day 2 Bus to Prague (4 1/2 bus ride)
Day 3 Prague
Day 4 Prague
Day 5 Bus to Cesky Krumlov (3 hour bus ride)
Day 6 Bus to Salzburg (3 hour bus ride)
Day 7 Salzburg, optional day trip to Hallstatt (2 1/2 hour train ride each way)
Day 8 Train to Munich (1 hour 50 min train ride)
Day 9 Munich
Day 10 Fly home

9 days is tight for all those places. Don't expect to linger long. You can work out a train schedule on your own to test the feasibility of your plan: http://reiseauskunft.bahn.de/bin/query.exe/en

Lubitsch appears to assume Munich as a base town for day trips to some of the other places (like Salzburg) in his/her comments. If you were only visiting Salzburg in Austria, then maybe you could day trip there from Munich as long as you don't have a lot on your sightseeing plate. I can't speak to driving there and back - too many time variables. But by train, only the RailJet trains make that trek in 1:30; round trip for two to Salzburg would set you back €150. So most people who do that route use the regional trains on a Bayern Ticket day pass (€31/2 adults,) which requires slightly slower trains (about 1:45 each way) so you're looking at 3.5 hours of travel time for a day trip. And there's another wrinkle - if you're doing the day trip on a weekday, you can use the Bayern Ticket only after 9:00 a.m. The first regional train leaving Munich's main station after 9 am is at 9:55. So that means you won't step off the train in Salzburg until 11:41. Obviously, you aren't looking at a full day for Salzburg.

So you will likely need to overnight in 4 places... Salzburg, Český Krumlov, Prague and Munich - and do a day trip from Salzburg to Hallstatt. (If you want to day trip to Berchtesgaden, that's doable from Salzburg as well. ) So you're looking at 4 major travel legs from Munich and back to Munich. Consider pre-booking those legs in advance at discount prices at the DB site (linked above) and the AT and CZ railway websites.

As for day trips by train from Munich to places like Nuremberg, Füssen, Mittenwald... you probably don't have time, but you can check the schedules. You'll again find long journeys and the weekday after 9-am restriction with the Bayern Ticket option. (It is possible to hit Nuremberg en route to Munich from Prague, however, if you're interested in Nuremberg. Note that DB offers bus service from Prague to both Nuremberg and Munich to shorten the journey. Český Krumlov takes a while to reach by train, as I recall )

On a recent trip, we hit all of the cities that you are interested in, however we were in the region for 3 weeks. With that said, I think that you are going to spend way too much time traveling from the various points, and you will not have a chance to experience or enjoy the cities mentioned. I would focus on Munich, Salzburg and Prague as there is so much to see and do in those places. Although Hallstatt is lovely, the village itself is overrun with day trippers. We enjoyed the Dachstein Salzkammergut area close to Hallstatt, but you would not have time for that. As for Cesky Krumlov, again the village is postcard pretty, but it too is overrun with day trippers and souvenir shops. In my mind, it's not worth the time or effort. Enjoy your trip!

Yes that is correct. 9 nights. Day 10 i'll be flying back early afternoon from Munich.

Thanks for the input thus far. Based on the feedback so far, it does seem i'll be spending too much time travelling.

How about if i do it like this,

Day1
Salzburg (Train from munich)
Maybe rent a car from here.
Day2
Drive to Hallstat
Day 3
Drop off the car at a nearest train station (Linz station?) and train to Prague
Day 4-6
Prague
Then train back to Munich
Day 7-9
Munich

Would this make my travelling time more manageable?

Thanks

Looks better. Not sure you have the days right, I think you have too many days in Prague. Spend 3 nights to give you 2 full days. So spend an extra night in Salzburg. You will be tired after a 12 hour flight, although maybe you can sleep good on airplanes. Traveling east to west helps.
Counting nights where you will stay:
Night 1 Salzburg, arrive Munich, train to Salzburg
Night 2 Salzburg
Night 3 Hallstatt, Drive or train to Hallstatt
Night 4 Prague, Drive to Linz and train to Prague, or train to Prague from Hallstatt
Night 5 Prague
Night 6 Prague
Night 7 Munich, Train or bus to Munich
Night 8 Munich
Night 9 Munich
Fly home

So Night 4 and Night 7 will be mostly travel. I don't know if renting a car will save any time as you have to spend time renting and dropping off. The train connections are not too bad. Also, Prague to Munich is fastest by bus. They are nice buses from what I hear, with bathrooms and wi-fi. The bus stops in Nuremberg first and it is only a 3 1/2 hour ride. Nuremberg is worth an afternoon if you want to stop and take a later train to Munich. Or just continue on to Munich. There is also a direct train from Prague at 9:12. Train is 6 hours, bus is 5 hours.

I don't want to discourage you but if you aren't an ardent clothing shopper that Ingolstadt village is barely worth a day of your precious holiday time. The historical center of Ingolstadt and the Audi museum would make for a day trip but then there are more attractive towns within reach like Landshut or Regensburg.

BTW. Get rid of your car as soon as you return to Munich. It's easier to do both your day trip and your trip to the airport by train. And please remember that you have to be at the airport 3 hours prior to departure.

Yeah i actually am only driving in austria. In munich will be mostly public transport.

As for ingolstadt, yeah there's only if we cant think of anything else that interests us.

Hmm, not sure why my last post went missing. Re-posted

damn...my updated re-post is missing again....looks like it was deleted??

Hi Guys! Trip is coming up in a month. I have booked a few hotels while planning the itinerary at each place for the day. This is what i have so far.

Is there any problems with this planning?

Day 1: Hotel in Salzburg,
- Arrive Munich, train to Salzburg, pick up car and start sight seeing in salzburg.
-Some of the areas i might be interested salzburg cathedral, mirabell palace, redbull hangar(maybe), mozart residence
For the night i will check in to a hotel in the Golling an der Salzach region.

Day 2-3: Hotel in Bad Mitterndorf (near Hallstat)
-Next morning, if there's nothing interesting in salzburg i will drive towards hallstat area.
-Activities will be exploring the Dachstein Salzkammergut different points, skywalk etc.
-Exploration of hallstat town area and the lake.
-Night will be at same hotel

Day 4-6 Prague
-Morning drive to Linz, drop off the car and train to Prague. Should reach prague by noon? Still need to book the train tickets.
-Night at a Hotel near old town.
-Prague castle
-Charles bridge
-Astronomical Clock
-Toy museum (maybe)
-St. Nicholas Cathedral

Day 7-9 Munich
-DB Bus to munich
-Hotel in Au Haidhausen area.
-Hofbrauhaus
-Marienplatz
-Glockenspiel Clock
-Nymphenburg palace
-BMW museum
-English Garden
-1 day of outskirt day trip probably

Day 10 Munich
-Prep for hotel check out and train or car to airport
-Fly home 13:10 flight.
-Home

Looking at the train schedule, from munich airport to salzburg i will have to take the S-bahn to Munich OST. Then transfer to another train from Munich OST to Salzburg HBF and discounted rates start after 930am.
Is that right?

Also, for the Linz to Prague train, i saw a notice on the obb website that states:
Construction work - Rail replacement services
Due to construction work no trains can operate between Linz/Donau and Rybnik(CZ) from 19/08/2017 through 10/09/2017. A rail replacement bus service is being arranged. We apologise for any inconvenience this may cause.

But i still can pre-book the tickets. Does that mean the above does not apply to me, although according to map the train will run through rybnik station.