If you have some apps on one pc and some apps on the other then you're going have a problem. If that's the case then you have a couple options
1. Move all the apps to one pc#1. In iTunes make sure the "sync apps" is checked on pc#1. On pc#2, make sure that "sync apps" is not checked. This will allow your device to sync the apps on the first pc and not on the 2nd. So when you plug phone into the 2nd pc, your apps won't get erased.
2. Move your entire iTunes library onto an external hd (I use this method). Then you can open iTunes on any computer and sync the iTunes library from the hd to any of your devices. If you're syncing with computer that isn't yours, you'll have to authorize that computer tonmakes sure everything syncs correctly. Your can then deauthorize the computer once your done.