Does anyone trickle charge batteries when not in use with the booster port under the rear bench seat? Or do I have to connect directly to the battery for it to charge? Wasnt sure with the batteries connected to all the other electric systems if the charger will work properly. Thanks

Makes no difference if you connect at that jumper cable plug or at the battery directly. That connection plug goes directly to your battery. So same difference.
If you wish, you can turn your battery switch off to disable all electrical items during charging. Only items pulling a draw will be your radio memory and the Mercathode system. Doubt enough draw to overpower the trickle charge, especially if you are out of the water so your mercathode isn't pulling any juice.

FYI that plug is the same one used on electric forklifts, thier batteries, and chargers. I believe it is a 350 amp plug used on 36v and 48v trucks. So you will have no issue with what you would like to do.

I don't have shore power and that is what I used to do every weekend.

I use two separate "float" chargers, one on each battery. They are 1.25 amp. units. This may be overkill but by hooking it up to the booster cable port you are assuming that both batteries need the same charge.
At $40 each an extra charger is not a big expense.

I have no issues, as long as you have a good connections no different then going direct to each battery. I charge my batteries at the end of every season and at the begining never had a dead battery yet or any issues through three seasons.

Bout the deep cycle batteries from sams 4 years ago and running strong.

Any idea where I can get one of these plugs? I'd like to make up some jumper cables since I don't have the factory ones.

I did the exact same thing. It's an Anderson Powerpole plug (SB175) for 4-gauge wire. I got them from Powerwerx.com. You will also need to buy the crimper tool though (Anderson SB Series Handheld Hex Crimper) unless you have one that will crimp the connections..

Bought a pair of heavy duty jumper cables... cut the ends off one side and put the powerpole plug on the other... unfortunately, the crimper is like $90..

Try like a fork lift supply or something you can probably find a cord with that end on there.

PM me, I have a couple of kits laying around.