Yeah, I think that how it would work. If you were to have 2 original series each series will generate each own ad revenue and just drop the daily earning all together at the end of the day in the same account.
It's like if you were using Google Adsense, you will just make one account, but you're running ads on two or more websites. All the earning from each sites will just come to that one account.
In your case, you might stop receiving ad revenue for your "fan comic," but you will still earn revenue from your "original comic."