I have not been on the Eastern Europe tour but it is on my short list! I have been to Vienna and Prague and loved both cities. I went on the week long Prague tour when RS had this tour and I spent four extra days in Vienna after the GAS tour last year and it was not enough. I would definitely look at the RS guide books for both cities, watch RS videos and others on YouTube for free to get the feel and know what each city has to offer.
I would love to go back to both cities. I loved Vienna and thought it was easy to get around, many wonderful museums and palaces and concerts and operas to attend to. I went to two concerts and an opera and the horse show while I was in Vienna. You can do something every night of the week in Vienna. Along with going to their amazing cafes and shops areas and museums. You can spend a week in Vienna and not see it all. Prague, it is a most wonderful city and there are several museums to see and the Charles Bridge is outstanding. Depending on your funds and your time you can stay for as long as you can in each city and see tons of things.
Is 3 full days enough in Vienna, no but if that is all you have then you will see a lot in that amount of time.
I don't have any knowledge about getting from Vienna to Prague.
But whatever you decide, Prague or Vienna to stay in before the tour will be wonderful. I would stay in Prague because your there already and leave Vienna for another time but that is up to you. There is much to see in Prague for 3 full days before the tour.
Have a great time whenever you go!