Issues syncing 2 iPhone 5's to iTunes on the Same computer

I just upgraded my wife and myself to iPhone 5's Previously we had the 4 and both Synced our phones on seprate computers.
With the upgraded phones, I decided to move the syncing for both of them to a newer computer (a third machine) I have not had two different devices with different Apple ID accounts on the same copy of iTunes before but was told by the Australian Apple support that this is ok.
Anyway, in trying to reorganize my Apps from the iTunes interface - it is apparant to that all Apps are mixed togerther in iTunes and as I delete apps from screen 11, more appear that were originally on my wifes's phone.
I hope this makes sense.
I just assumed that when one phone was connected - only Apps purchased with that Apple ID would be available in the iTunes apps interface.
We share the same iCloud account for syncing calanders and contacts - but the apps were bought on different Apple IDs
I am just worried now that I have spent an hour rearraging things to my liking - when her phone is next synced - that it will screw hers up or screw mine up the next time I snyc after she does.
Can anyone tell me how iTunes manages multiple devices with separate Apple IDs on the same copy of iTunes one computer?
Thanks
I am runinng iTunes 11.01 (12) iOS 6.1 and the Machine is running 10.7.5

Let it sync then restore as a new iphone.
http://manuals.info.apple.com/enUS/iPhone_iOS4_UserGuide.pdf

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Message was edited by: tmartine

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Issues syncing 2 iPhone 5's to iTunes on the Same computer

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