Time Machine's thinking is backup everything except what you tell it not to and the time machine hard drive itself. It should not matter how many drives you have connected, they should all be backed up to the time capsule just fine. In other words, you can backup multiple sources but only on one destination, as long as this destination shows up as a single logical drive in the Finder.
Just check in Sys Prefs > Time Machine > Options if the other HD isn't just simply added to the list of exceptions, don't see how it would end up there by itself, but just in case.
And I don't think you can keep working with the same backup, since you divided the data in to 2 separate logical drives. Time Machine just does not think like that. Better start from scratch, perhaps backing up the current backup set to another drive if you need to preserve all the previous backups... Some people need to be able to go back in time to a specific point. I care only to have one up-to-date copy, don't care much about having 30 different ones.