Hmm. Have to disagree a bit here.
A battery is a DC device. For the chemistry to work out, the electrons have to physically move between anode and cathode. While an AC current can move power across short distances of dielectric (think capacitor) a DC current stops and electrons stop moving as soon as the voltage in the capacitor is the same and opposite of the driving DC voltage. A good capacitor has huge surfaces and very narrow gaps, unlike a battery near water. (If you set a bare battery in water, it may help keep salt and acid crystals moist on the battery body, creating a path for weak discharge currents between the poles. Plastic battery boxes do a good job keeping water out...)
As for the relation between concrete and batteries, it's widely considered an urban legend. I still wouldn't store batteries on concrete unprotected - in case of a major leak, I'd have a memorable hole in the floor.
Because of the possibility of leaks, you should always have a box for your batteries, whether built-in, or one of the portable plastic jobs. And you need to strap down your battery. For a setup like the DSII, for those that don't want to construct a battery box, building a battery well seems like a good alternative.
On my DS1 I don't bother with that and simply rest my battery boxes on the floor in front of the benches, secured in place with straps. The cuddy floor is a dedicated "passenger compartment" and I don't take my batteries with me every time I go out - less than half the time, I would say -- so keeping them where I can access them when the boat is on the trailer is a huge plus. In between, the batteries in their boxes sit, you guessed it, on the concrete floor in my garage, where they get recharged about every other month, which seems to work out fine.
I'm surprised your autopilot is so sensitive, but if it's just a trolling motor, I doubt that +/- 2ft will make an observable difference. Adding 16% of the distance should increase the total voltage drop in the cables by 16%, or 1/6th. If you've kept your voltage drop small to begin with, this 1/6th shouldn't have any observable effects.
I used to run my motor by moving a battery back, that was before I added a cable run. I've tried it, and I can't see the difference. There's too much "noise" in the real world - different wave action, wind direction, strength, differences in the trim of the boat, etc. for any small change like that to "show". (OK, perhaps if you had trolling motor races between otherwise strictly comparable boats.).
Anyway, sorry for being so "disagreeable" today.
