You will love the "free" (after cost of installation) AHs your batteries get anytime the sun is shining. Plus, when in storage your batteries will keep/remain charged.
If you don't think you will add more wattage in the future, getting a 30amp controller will be fine. If you think you might want to add more panels in the future, then you should look to buy a 40-60amp controller.
As mentioned, you 100% need to get an MPPT controller, otherwise you will only get ~40% of the watts that you are expecting/hoping out of your panels.
Since you have two separate battery banks, it would be kinda cool if you incorporate a switch of some sort such that you can charge either (or both at the same time) bank that you want.
Parallel vs series probably won't make much difference overall. In either case, you should install them away from any tall items (ie. AC unit) on your roof.
Good luck!
Chris
San Jose, CA
Own two 2015 Thor Majestic 28a Class C RVs