Syncing an old iPod Touch (1st Gen) and new iPad (3rd Gen)

I have an old iPod Touch (1st Generation) which runs iOS 3.1.3, the latest possible for the device. It is synced to my Windows desktop PC. However a lot of apps are not fully updated because the newer versions are no longer iOS 3 compatible.
I am getting an iPad (3rd Generation) on launch day next week and will obviously need to sync it to my PC with fully updated apps, however, I also want to keep using my iPod Touch will all its apps too.
Is it possible to have two sets of apps on iTunes on one PC, one for the old iPod Touch with its older apps and one with the new apps for the new iPad.
I update all the apps on the iPod Touch itself so I never update an app that is no longer compatible with iOS 3.0
The solution I've come up with at the moment is to copy the iTunes folder on to my laptop and use that for one of the devices and use the desktop for the other. But would like to use just one PC if possible.
Can anyone advise?
Thanks

It turns out that I took all the apps off my touch, but I have an iPhone 3 that hasn't been updated in at least six months.  There's got to be something on there that's incompatible with the current iOS architecture, but it's syncing as I type this with no problems. 
You've got your iTunes copied to your laptop - why not use the original copy for a little snooping?  I think you'll find that everything works just fine.
BTW, there are several apps in the iTunes library on my desktop that are duplicated.  I never could figure out why, but my guess is that some of them are versions that will run on one handheld and not the other.
Hope that helps.
Mike

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