The two banks are charge separately using the same controller and solar panels.
Multiple solar panel controller.
Sealed gel flooded and lithium.
For mppt controllers mppt tracking of each subarray is preferred as there is less impact with voltage mismatches.
Mismatched specification panels will always lead to a compromise in performance.
If i were you and because solar controllers are usually a lot cheaper than solar panels i would buy another solar controller and operate each panel separately.
In fact xantrex makes a communication cable to wire between controllers to do exactly that function.
If you have more panel wattage than your controller can input then you must use 2 or more controllers as separate solar panel arrays.
However there is no problem for multiple controllers to serve a common battery if that is what you want to do.
There are different sized charge controllers that are designed to handle varying amounts of solar panels.
Mppt controllers have a switch mode buck converter.
The connection of multiple solar panels in parallel arises from the need to reach certain current values at the output without changing the voltage.
Most solar charge controllers will only allow you to charge one battery.
In fact by wiring several solar panels in series we increase the voltage keeping the same current while wiring them in parallel we increase the current keeping the same voltage.
Cheap charge controllers are a bang bang mosfet switch so either the battery is straight on the solar cell or not.
Once the battery is full the charge controller switch will be mostly off so the other charge controller can use the solar cell.
To meet high power charging requirements several solar controllers can be connected in parallel to a battery bank with each controller connected to its own separate pv subarray.
Two of them on one panel will get very confused.
Charge controllers regulate the electric current that is transmitted to and from solar panels which prevents overcharging and increases their lifespan.
Ideal for small and medium size arrays.
You can wire up to four 12v solar panels in series 12v solar panels usually exceed that voltage hence the limit of 4.
Auto identifying 12v 24v dcsystem voltage also compatible with various deep cycle battery options.
There are a few charge controllers that have now added the default option of having two battery banks.