Any solar experts out there

I have 2 12v 100w solar panels that I want to use to charge my 2 12v batteries wired in series for my 24v trolling motor on my boat. My question is can I just charge each battery with its own panel and solar control charger at 12v without any issue?

 

You should be good as long as the 12v batteries are not wired in series while charging.

 

What charge controller do you have? Many will do both 12V and 24V systems. You'd just need to wire your two panels in series as well if your controller is capable.

 

I ordered cheap controllers that are capable of 12 or 24. I have a on board charger and top the batteries off when I'm done but the car port I keep my boat under is far away from power to keep batteries topped off. I already have battery tender hookups to each battery from before the on board setup and was thinking sometimes when not charging the trolling batteries I could charge the starting battery with one of the panels.

 

The starting battery is separate from the trolling batteries? If so, then yea there should be no issue at all charging it with it's own solar setup.
The two trolling batteries however, it's better that they always be treated as a single 24V battery (they should also be the same kind and age), otherwise there is potential for their charge levels to get out of balance, possibly damaging one or the other during use or while recharging.

If your charge controller has auto voltage-detection, then it should be real easy:
Connect the controller to your battery (or batteries, if 24v), then connect your panel(s) to the controller (be sure to do it in that order though). Use both panels in series for 24V, or one panel alone for 12V (you also could use both panels in parallel for 12V as well).

 

Yes the trolling batteries are isolated to just the trolling motor. Just was wondering if possible to use as battery maintenance for both 24v system and 12v system but it might just be easier to just wire as 24v for trolling setup and just get another panel for the 12v system. There trolling batteries are brand new so I rather not worry about an imbalance issue.

 

Yeah in that case I would definitely get a separate maintainer for the 12V.