I have a marine battery charger with the alligator clips. When i charge my trolling and cranking battery i have been unhooking them and taking them out of the boat to chargeone at a time. All the electronics are hooked up to cranking battery. Do i need to unhook the batteries and take them out of boat when i charge them. Or can i just hook alligator clips up to them as is and charge. It is a pain to take them in and out so if it is not necessary to do so i would rather not until i get an onboard charger. I am mainly worried of damaging anything hooked up to batteries when charging. Any input would help. Thanks

No need to remove your batteries.  I charged my batteries with a black and decker smart charger for years with clips.  I would hook up the engine battery first and it would charge in a couple of hours.  My Javelin had dual trolling motor wires running to the front plug where it was jumpered over to go up to 24V. I would clip the alligator clips to a spare trolling motor plug wired up to posts and wired to flow 12V back to each of my separate trolling motor batteries.  I would let this go over night and both batteries would be charged in the morning.

Yup, as long as you're on the terminals of 1 battery at a time, you're good to go. Leave em in and hooked up and charge away.

One thing you need to make sure you never do, crank your boat plugged into a charge system. Ive seen it smoke two controls. Maybe newer boats have down the line resistors, but the older ones usually do not. Those little wires near the helm cant take a pile of juice.