PolyMorph and ShapeLock both look like versions of Friendly Plastic I used to use for sci-fi props a couple of decades ago.
It works great, and can even be removed from electronics after you've put it on (by melting it in a double-boiler, since it floats and the electronics usually sink), and is very hard and resilient at first. Unfortunatley after exposure to UV (sunlight, especially), it tends to get fracturable, and cracks or shatters when dropped on hard surfaces. So I ended up potting the electronics in silicone, and *then* putting FP around them, for things I didn't want to have to cast things in molds for, but rather to hand-shape (great for ergonomic designs, since you just mold it with your hands to fit the way you want, before it cools too much).
Another problem with it is that since it is meltable by low heat, leaving it in a car in summer is a REALLY bad idea.
As long as you can do the work with SMT, it should all fit. It may take some creative routing of traces around the board to get it all as compact as possible, including components on both sides (primarily to use the SMT caps and resistors as jumpers across traces that would otherwise require either more layers or more plated-thru-holes for going around things).
A Li-Ion or Li-Poly battery would save a lot of space compared to boosting AAs or even AAAs, and net you a lot more power, I think. If you can get a LiFePO4 battery in the flat pack size you need, it will be even better, because it isn't going to potentially destroy everything if something goes wrong with the charging circuits or battery, or if it gets wet/etc. Unfortunately it doesn't have the same power density as the others.
I've done a very very little searching for this type, and haven't found them yet, just what are listed as Polymer Li-Ion or Li-Poly flat packs, such as the ones here:http://www.batteryspace.com/index.asp?P ... tegory=869
and here:http://www.batteryspace.com/index.asp?P ... egory=1338
(these two pages used because there are images of lots of shapes/sizes, and a table of measurements and weights)
I wanted to use them for my bike helmet lighting, if I could find them, but all the LiFePO4s I've so far found are typical cylindrical cells.
There are also places that sell just the BMS boards for these batteries, such as here:http://www.batteryspace.com/index.asp?P ... egory=1356
(since I was already at the site for the above, not recommending any specific place)
So you don't have to design your own. But you can do so if you want to integrate the BMS/charger into the rest of the main board.
There are also of course the standard battery packs already made with built-in BMSs, such as celphone or other devices' replacement batteries. (in fact, old batteries from such a device are a place to get BMS boards from, to use with bare batteries for experiments, if you need to).