Those are actually great questions. I just dump the whole thing in a styrofoam box (that fish were shipped in) and pick out the pods to put back in the sump(yes I'm OCD)

. I usually fill the cup about 3/4 full with the polyfil. If you put too much and pack it it will stop up quickly, trial and error here. I do not add more when it gets wet and compresses. I take that in to account when I choose how much to put in. It will tend to make the cup float up until it get's wet and compressed a little, usually just a few seconds.