Managing apps for multiple users in one iTunes library

Hi - my wife and I both have iPhones and separate iTunes ID's. We both share music in one iTunes library and sync to the same library. We also backup our phones to that same computer. We have some apps on both phones (for example, Pandora) and when we backup/restore our phones, iTunes apparently will put "my" version of apps on her phone and "her" version of apps on my phone. Afterwards, when I update apps, my phone will ask for BOTH my iTunes ID AND her iTunes ID. Similarly, her phone asks for both her ID and my ID. Presumably, this also uses two of my FIVE authorized devices, which is also a problem.

My question is how can we manage our apps separately on iTunes so that we can get rid of this annoying behavior? It is very common for families to share one common iTunes library, so I don't see why this would be unsupported.

Thanks for any assistance!