I was considering a few options for what to make my battery trays out of - I think I'm going to use what I've used in a number of other vehicles:
PVC u-channel
The price I see on Amazon right now is very low - I bought a bunch when Amazon had it even a little cheaper. I want to fit these batteries in on their sides:
http://www.hobbypartz.com/98p-25c-4000-6s1p.html
and my 5s packs of the same capacity are 41.5mm tall (a little less than their specs). So I sanded down the inside of one leg of the u-channel with my dremel drum sander - and the 5s packs are a perfect fit:
I still need to cut slots for the battery leads and then I can lay them out where I want them on the chassis. I plan to run 2 6s packs in parallel.