Not a silly question at all--I was so confused by pockets at first. I just discovered FB today. I got my first one in the mail and I love it. So light and trim but no leaks. Definitely the "Cadillac" of cloth in my opinion.
Your liner (insert) goes inside the pocket. What kind is it? I use Thirsties, which are 3 layers of microterry but they feel pretty thin. Anyway, the urine will go straight through the fleece and be absorbed by the insert, and the fleece will stay dry. This is supposed to be the case with all pockets but I have had the best luck so far w/ FB. Dd wore hers today for three hours and the fleece was completely dry, although the insert was soaked when I took it out! I ordered a dozen more immediately!
You can put a prefold or anything else you want inside the pocket to increase absorbancy, especially for overnights. I still use sposies at night. I hate to put more than one insert in a pocket because it looks so bulky and uncomfortable. But I am in the minority here! I wouldn't put a prefold or anything else on top of the fleece because then your baby would feel wet, and the point of the fleece is for her to feel dry.