You can do this if you want to be sure about what you are syncing. Turn off auto syncing in iTunes.
Launch iTunes and got to Edit>Preferences>Devices>Prevent iPods, iPhones and iPads from automatically syncing - check that box at the bottom. Click OK. Quit iTunes.
Now when you connect the iPad to the computer, iTunes will not sync until you initiate it. You can click on the iPad name on the left side under devices in order to select the iPad and then click on all of the various tabs within iTunes and select the unique content that you want to sync from that ID.
Now to be clear - you cannot have one app and use it with two different ID's so that you can have two sets of app data associated with that one app. For instance, if you bought Pages the Apple word processing app with both ID's - you cannot have two sets of files each associated with each unique ID. All of the data and files have to be consolidated into the one app backup.
However, there are other users that use two different ID's on the iPad. I really think that the only issue is to make sure that you use the correct ID when you sync and update apps. It's not like you are using two iPads with one ID and you want to have a different sync configuration on each device. You have one iPad using two ID's, so you do want all of the apps to sync every time. If all of your apps do not sync each time - you will lose the data associated with the other ID.
Read this discussion in which I participated as well, but read the comments from Dah*veed about merging two ID's into one iTunes library.
https://discussions.apple.com/thread/3864828