Two of my batteries are wired in parallel to keep 12v...but have a bigger bank. Can I still run separate charge leads to each battery? To me it would be charging that "bank" two at once...is that a bad thing?

Or do I need to get a batter switcher to keep them from being wired together?

Simple answer is yes you can. If you want to put a switch in, that's fine, but unnecessary. Alternative is to connect one changer to + on battery one and - on battery two. This keeps the charging rate the same between the batteries, but will slow down the rate of charge if only using one bank from the charger. Just do a search for parallel 12V batteries, 2 chargers.

Yes works fine just hook each pair of leads to each battery

An interesting and I don't know problem.

Since they are in parallel, the first charger sees the whole system as one. The second one the same.
That also means the two battery chargers are connected to each other.

You can safely charge them both by just pulling one connecting wire off and then charging them as two separate batteries using both battery chargers.

This is exactly what I do and it works like a champ.

If I do this...do I just leave one bank on the charger unhooked?

Or do I put two +'s on one battery and two -'s on another battery?

Use all three banks. You can even use all three banks on one battery. It will charge 3 x faster.

In the parallel set of batteries, you can connect both (+) leads to battery ones positive, and both (-) leads to battery twos negative. The jumpers between the two batteries will complete the circuit and will allow the batteries to obtain a similar charge state.

Don't overthink this stuff.

I have a similar ? and don't want to start a new thread. I have a MinnKota battery monitor that only works on 1&2. Previous owner lied when he said that number 3 was not hooked up. OK maybe he forgot. Number 3 will not display. I think battery tenders are PNP but not sure if there is some setting that has to be switched to monitor 3 batteries.