I'm taking a vacation to Germany and Austria with my wife, parents and in-laws. One couple will likely spend more on dinners than the other two. This could be a hot button issue (but thankfully the only one I hope!)

Anyone think I'll have a hard time getting the wait staff to make separate bills?

None at all, this is very common.

Vocab help:
"Getrennt" = separate bills please
"Zusammen" = all together -> one person pays for all

Sit at different tables?

This is absolutely normal in Germany and Austria. I'm a member of a women's group that goes out to dinner every month in Stuttgart. There's usually 10-20 of us and it is never a problem for each of us to pay separately. The waiter comes around, you tell him/her what you ordered, he/she adds it up and tells you the total, you add a few Euro tip (usually round up to the nearest 5), and pay on the spot.

I have been successful with
Ich möchte getrennt bezahlen.

I don't know how colloquial or grammatical it is, but the waitress obliged.
Then it turned out that she could chatter away in English with good accuracy.
Sort of funny when I think about it because her English was good enough that had any of the group made derogatory comments, she would have understood them all!!

Americans who visit Germany and think that all the people in stores and on the streets cannot understand them are living in a dream world.