Mac – Can the Time Capsule back up multiple drives (internal and external) at the same time

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.

Yes, Time Machine will backup until it fills the backup disk and then it will start overwriting old backups to make way for new ones. However, if the volume of data you've told Time Machine to backup exceeds the size of the disk Time Machine is using to save the backups on, it will complain that the disk is too small. If you have a Time Machine disk which is smaller than the combined size of the hard disks used by your Mac, it's likely you'll need to manually intervene at some stage due to this issue unless you're very diligent about ensuring that you don't ask it to backup too much data.