They should be stuffed lightly. The "ideal" amount is about 1.5 pounds of polyfill per cubic foot. The stuff is sold in bags marked in pounds, so it's pretty easy to figure out. Just don't pack it in there, that'll be too much. Whatever fits in loosly and easily.
Polyfill can be used in ported boxes. Almost all manufactures suggest some sort of damping material when running ported, usually a sheet or mat attached to the sides of the enclosure (simular to 1-2" thick home insulation, for a visual). I had nothing of the sort, so I very lightly stuffed my enclosure with polyfill. My sub and port are on opposite ends of the box, so I just put the material in the 2/3's that the sub is on. Seems to work fine. I did it on my old box with my JL 8 W-0 and it worked very well, seemed to lower the tuning a noticable amount, gave a stronger low end (I was very surprised, I was just trying it for kicks and grins).