Do you have a main motor? Is it a 4 stroke? If so, you can idle your main motor for a while if you are worried, as they don't load up. Most 4 strokes have a heavy duty alternator and can take care of your issue.

Trolled for 9 hours yesterday with stand alone batteries running the riggers and pot puller, and they had no issue. The batteries were not tied into the motor's electrical system, so they did not get recharge. We also didn't pull each rigger 50 times from 150 feet. The amount of use might be an issue.