Take a look at the new skimmer just released from Sapphire. nanotuner.com should carry it. Fits perfectly in the middle chamber without cutting or trimming and still allows the lid to close. (Not all skimmers used in the 29g BC allow this)
Anytime you use carbon, purigen, chemipure, etc you want the water to flow THROUGH it. Don't just throw a bag in there. Position it in a way so the water must be forced through the mesh bag. For example, place it where the square blue sponge that came with the BioCube is. Water must be forced through it to pass from chamber 2 to chamber 3. If your tank is cycling, it wouldn't hurt to add some now. But if the cycle is complete and your tank is just sitting there as a big box of water, I'd wait on adding until you add livestock.