Syncing two iphones on itunes

I used my wife's computer to sync my iPhone4 (since my laptop was in the shop and I hadn't connected to iTunes to upgrade software). I went to the Apple Store and spoke to someone at the Genius Bar (or service counter?) and asked about using ONE itunes to sync TWO separate devices. Again, I needed to sync to get the latest update to the iPhone4, at that time.
Well, I was assured that there wouldn't be any 'crossover'. What's mine would remain mine; what's hers would remain hers.
That isn't completely true. ALL of my apps are in iTunes and her apps are on my phone.
I just wanted to sync my iPhone, back up MY apps, NOT get my wife's apps, and keep the iOS current.
The advice that I got helped to create a mess. It's not a serious FUNCTIONAL problem. But, it's quite a bit annoying. (I have TONS more apps than the wife and our social media interests are VASTLY different.)
Any advice on how we can clean up this mess AND avoid it, in the future, even if we share the same laptop to sync?

How to use multiple devices with one computer

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