Setting up for multiple batteries trolling

I am in the process of buying some new batteries, taking one deep cycle ( one year old) I have been using for the trolling motor and now going to be using this battery as the motor battery and depth finder battery.

I want to add two deep cycle batteries parallel, the distance between the batteries will be less than 4 feet (one in each dry box) to keep the boat ( 16' Lowe) balanced. I was planning on running a #6 gauge wire from one battery to the other, positive to positive, negative to negative.

What class battery would you suggest? Also will charging these batteries have any issues connected in this manner?

You shouldn't have a problem with the batteries or charging that far apart.

As to size, it depends on how you fish. A single 24 would give you 120-134 minute RC. A single 27 would give you about 160-180 minute RC. A single 29 or 31 gives you about 205 minute RC. A pair of 24s would give about 240-270 minute RC. A pair of 27s would give about 320-360 minute RC. A pair of 29s would give you about 410 minutes.

thank you CatFan I should have also said that size should be one of my considerations due to the amount of weight. I looked at some deep cycle last night and 27's did not see any 29's.
I like to long line, drag and sit at times, even do a bit of wading when its the right time of the year, the battery needed for wading though replenishes itself every time I feel that tug.

My :twocents. If you're talking about a 12v motor separate the batteries with a battery switch. A weaker battery will draw down the stronger one, keeping them separate eliminates that issue. You're also able to disconnect the batteries via the switch while not in use which will prevent any drawdown. If you're using a single bank charger you can set the switch to "both" to charge both at the same time(or run off both if you choose).
I was running 2 parallel and when I put the switch in it made a bunch of difference. Also went with 4ga over the 8ga I originally had. The switch and the wire add some costs but not that much in the long run.