Get a battery switch........I have mine set up to charge when I am running then I can isolate the mains/trolling system for trolling with the flip of a switch. Perko makes a great one I have used for years.....

As for amperage limits.........AGM and Gel type batteries do have to be charged at lower rates than wet plate cell construction. The reason for this is that a battery gives off hydrogen when charging. Glass mat style batteries (Optima for example) will form hydrogen gas bubbles in the gel that is between the plates. With no way to escape it effectively kills the battery at this location. Wet Cell Plate batteries, however, can easily expel this gas through the liquid sulfuric acid.

Battery manufacturers can give you an optimum charging rate for all batteries to prevent damage.

Another jewel I have found is the Vector Portside "Smart" battery charger.
This charger monitors the battery and properly adjust the charging rate based on the charging needs of the battery. It ranges from 30 amps down to a float charge mode throughout the cycle. No risk of overcharging.

It also has modes for "AGM" "Gel" and "Wet" cell style batteries......all have different modes of charging.

It also has modes for desulfating the plates, and balancing the cells. This is great for restoring the electrolyte balance in the cells and in some cases will revive even a "dead cell" in a battery.

My trolling motor battery "Trojan" manufacturer of Minn Kota batteries is about 5 years old now and is as strong as the day I bought it. I charge it regularly at 10 amps and if I am in a hurry 30 amps. The Vector charger does a great job of maintaining it without damage.

The biggest problem with battery maintenance is keeping the water full.

I run Trojan Wet Cell on the trolling system and Die Hard Platinum Marine batteries on the mains..........She always cranks when I say go!

Last week I couldn't even spell Injunear........Now I R 1!