We took my buddy's Bowfishing rig out for the first time last weekend. We were able to fish for about 3-4hours on 2 27 series batteries wired together for 12 volts. Is there a way to hook both batteries to the motors charging system and keep them charged up all night?

I have my boat rigged up the same way but I ran wires linking the starting battery to my two 27 series batteries with a switch between them. I went out the other night without charging my batteries frome the weekend and when they died I flipped the switch and started running the lights off of the starting battery. The extra battery added about two hours of run time before they were all dead. However my starting battery wasn't fully charged ether. The charging system can not keep up with the lights. I would suggest adding a battery to your bank

I am running 10 48 watt lights on two 27 series batteries. If I charge them before a trip they will last 7 - 8 hours. The batteries iam running are the cheap exides from academy. Bought two on sale for around 70 $ a piece. If that run time isn't enough I can flip that switch and run off of my starting battery but as soon as the lights start to show sighs of low power. Shut them off so you don't get stranded. When my batteries are dieing my led lights start to flicker.

Here is a pic of my setup

Nice setup. We were running 12 lights and when the battery's got low the ones with longer wire runs dimmed and then went out leaving us with fewer and fewer lights until the battery's were completly dead.

Is there some type of better charging system that can be added ? Our other idea was to buy a little honda 2000 generator and an ac to dc converter to run them .

I looked into the generator and convertors. But the cost was to much for me and you have to be careful to not get those converters wet. If you want to go that route check out powermax converters. But you might be better of adding a battery or two. You might want to go pick up a few 12 volt golf cart batteries.