My wife and I had this issue. What do you use for contacts? We use Google and what I ended up doing was turning off the "sync contacts" in iTunes and using Google sync which works great.
Originally Posted by Ringfinger
The problem we had with iTunes was that if you left the box checked it would over write contacts from each phone. It was a mess. I suppose you could leave the box unchecked and then check it and make sure it's syncing from the right contact list. I don't know, Google sync was easy and it works very well.