Are there any gotchas with using two Apple IDs for one user in the App Store?
There are a couple of gotchas I'm aware of.


If you buy apps on both iTunes accounts, they all get listed together when updates become available, not just the ones on the account you're currently signed into.  So if you click 'download all free updates' iTunes will only download the updates for the account which is signed in.  This can be confusing because you've told it to download all free updates and it doesn't tell you why it hasn't downloaded the others. 
If you have an Apple TV and you want to use Home Sharing, then you can only share the content for one account at a time.