Yes you can fit 2 batteries under the seat of a defender 90, i have 2 numax batteries a x-eng split charge system and a isolator.
I ran the the live cable to the isolator positioned on the front of the seatbox and then out of the seat box along the side of the chassis and then along the top of the chassis in the engine bay to keep it away from the exaust and around to the winch. I also ran a neg or earth cable the same route all of the way back to the battery. Most problems with winches are becausethey dont have a good earth.
Before you fit the 2nd battery you will either have to buy or make something for the batteries to sit on, i used a bit of 2mm plate with a bit of 25mm box section running the length of the seatbox(north to south) and then cut the plate to fit over riveted on to make the bottom of the seatbox flat. Once the batteries were i a used a bit of 6mm bar to clamp them down using M6 screwed rod( 1 at each end and one in the middle)
I squeezed the X-Eng split charge in near the back of the seatbox near where the the earth cables exit.
It all fits good, what i did do was use a piece of 10mm pipe to insulate the batteries from the screwed rod, i also covered the battery clap with adhesive foam to protect the battery,
Before i fitted any of that i used the wire brush attachment on an air die grinder to clean up the seatbox, Hoovered and degreased before painting with red oxide once that dried i gave it a health coat of waxoyl,