chumby is filled with both. There is a bag of polystyrene beads in the bottom of the chumby to give it some weight and balance (these are the same beads used in beanie babies). The rest of the chumby bag is filled with standard Poly-Fil, the same stuff used in plush toys.
You'll probably want to keep the fill away from the daughterboard as much as possible, as you don't want beads or fill to get stuck in a connector or the power switch. It won't harm anything electrically if fill comes in contact, but it might be inconvenient if you have to pry loose beads or fill out of somewhere it wasn't supposed to go.
The other thing you could do is just wrap the daughterboard in some electrical tape or heat-shrink tubing to prevent any fill from getting in contact with it. Then, you wouldn't need to contain the fill in any additional baggie.