OK, I have seen a few buried posts re battery placement, and a few have said they pack the battery in tight with foam. As I use two 18Ah AGM batteries, I'm thinking of making a mounting tray with a padded, non-slip bottom that can be pushed down from the rear hatch to just behind where the hull dips for the seat. Then I can pack foam at the sides and top to prevent movement. This would work except in the worst of roll-tilt-flip-explode type situations on the yak, I think. It also leaves the rest of the cavity for other storage.
I was intending to get a 35Ah battery, but it is too awkward to handle into the hatch. Easier with the 2x 18Ah smaller ones. From experience, I get about 1.5 hours full power on one small battery with the voltmeter dropping from 13.6 to 12.7V, so three hours is plenty out of two. And they are certainly not drastically discharged.
I have also looked at marine type fittings for the outside of the hull to plug the motor in to. There seems to be a reasonable range of stuff, though expensive. That's something else to research on eBay.