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I just finished mounting a battery in my 13' for a trolling motor and I researched it quite a bit.

You should use a battery box if the battery is out in the open. My installation is under the seat adjacent to the helm so I used a battery tray. There wasn't enough height to allow the box to fit. Attwood and Seasense make decent boxes. You can get either at Basspro or Cabela's online.

Mounting is a bit more difficult. I have no wood under the location I needed to use. I'll just tell you what I ended up doing. I first drilled holes for the mounts with a 5/16" drill bit through the floor. Then I fashioned a tool using some 1/4" threaded rod and shaped it like a "Z". I used it with a shop vac to remove some of the foam below the floor. I ended up removing about 3/4" deep and 3 to 4 inches around each mounting hole. Pretty easily done actually. Once the foam was removed, I loaded a large syringe (you can find these at ACE hardware in the paint department) with pre-mixed marine grade epoxy and injected it below the floor through the hole. You have to run a piece of wire in and out during this proces to make sure you don't have any air trapped under the floor. Once the hole is full of epoxy to the brim, let it cure. After it is cured, pre-drill for stainless screws. Make sure you use 3M 5200 sealant on the scres when you put them in to seal it from any water and improve the grip. You must drill the right size holes for the screws, not to big, not too small, or you'll crack the epoxy or strip it. This is critical. I cured a couple of wax cups with epoxy in them to try drilling a tapping before I drilled my boat!

Get the "footman Loops" from these guys to strap the battery down. These are stainless and very similar to ones on other Whalers- http://store.ryansproducts.com/1folostst.html

As far as I am concerned, the best straps in the world are the YETI straps from YETI coolers (also online).

Good luck with your 13. Best boat its size anywhere.