Driving Wachau Valley from Vienna, and on to Salzburg and Hallstatt

It might be helpful for Hallstatt, but you can get to Melk easily from Vienna. We bought the train, boat combo ticket and it worked like a charm. Train to Melk, river cruise to Krems, train back to Vienna. And since you'll be coming in on that side of town might I recommend stopping for dinner at a Heuriger.

I've done those areas by car when I had the car for a months-long lease. It was a nice convenience, making extra stops easy for photos, picnics, hikes, ice cave, etc. The car is a little easier for getting to Mauthausen concentration camp memorial, which is otherwise accessible by train + taxi, but you have to take your luggage all the way to the visitor's center to store it (none at train station).

If you take the train all the way to Vienna for the first leg, then car rental from there back as far as Salzburg, that keeps the car rental entirely within Austria an avoids stopping twice in Salzburg. From Salzburg to Munich Airport takes 2.5 hours by train.

As Laura mentioned, best is to go straight to Vienna and work your way westwards ending in Salzburg before going to Munich.

If you have not booked your airline tickets yet, compare different flight options and prices. It could make sense (pricewise) to fly to Vienna. Check if a return flight, even when skipping one leg, is cheaper than an open jaw flight.

E.g. United CLT - IAD - VIE, return VIE - MUC - CLT (skip first leg)
Lufthansa CLT - MUC - VIE, return VIE - MUC - CLT (skip first leg)

Best search engine for flights: https://www.kayak.com/flights

Should you get an ultra-cheap return flight to MUC, still consider taking a flight to VIE (about $130).

I am also from NC and we always fly CLT to MUC to VIE. I suggest flying to VIE. Make a day trip to the Wachau (rent a car for the day or take the very easy and efficient public transport). This way you can visit the Wachau on a good weather day. Take the train to Salzburg with Westbahn (this stretch of highway is horrible for driving). Rent a car in Freilassing, which is in Salzburg but in Germany, so you’ll avoid drop off fees. Drive to Hallstatt, Salzkammergut, etc. Taking public transport or a tour is also a very viable option. Take the car or train back to Munich. I do think dealing with parking and traffic maybe be stressful with a car.

Take the train to Salzburg with Westbahn (this stretch of highway is horrible for driving).

I don't quite agree with Emily's assessment of the A1 Autobahn (freeway). I had been driving that route several times. It is a busy road, but became better and better over the years because an additional lane was added piece by piece. Compared to US the style of driving in Austria is different, though. But if you got acquainted with it, driving is easy. (By traveling through different European countries I learned that in every country there are specific driving habits.)

The train is a much faster way to travel between Vienna and Salzburg than by car. I have also driven the A1 stretch numerous times and always hit traffic, accidents, construction.

Hallstatt works by train, too. There is a boat, the Stephanie, which meets the train and takes you across the lake to Hallstatt. Fun and beautiful!

There is no doubt that the train is faster for going from Vienna to Salzburg, and I am the least to favor car traveling in Austria, unless absolutely necessary.

But given the towns the OP wants to visit, taking time constraints into account, it would make sense to start the trip right in Vienna and continue westwards by car without going back and forth.

Although a day trip to Wachau valley is doable by train/boat/bus it is more convenient to set your own pace. I love Dürnstein, walking around in the medieval village and along the Danube, having a good lunch there, and always climbing to the very top of the fortress' ruins for the magnificent view.

You can continue then to visit other villages like Weißenkirchen or Maria Taferl, and most prominently the abbey of Melk. In Linz you can make an overnight stop, visit the Ars Electronica Center, and make your way to the Salzkammergut (Gmunden, Bad Ischl, Hallstatt). After staying another night there you end up in Salzburg, where you return the car (don't take it to Germany).

After having visited Salzburg you go by express train to Munich. It is always better to arrive some days ahead of departure in the town where your flight leaves.