Currently Being ModeratedJan 29, 2013 7:32 PM (in response to dietraw)
If you're are using the same AppleID, then it's easiest to sync them from the same user account. iTunes will recognize them as two devices and allow you to set each up the way you want to.
If you are using to different AppleIDs, then it's best to sync each to a different user account, with the iTunes logged into the correct AppleID on that account.
Note, you will only be able to run Match or redownload purchases for one AppleID per computer.