Bottom tray is for the sponge top tray is for bio media. There is actually quite a bit of room in the trays so you could even do sponge and carbon pack in the bottom and the bio on top. I am pretty happy with mine. There are a few design features I wish were a little bit different but once you become familiar with the filter maintenance is pretty easy. Just make sure your trays are seated properly as well as the ring on the impeller housing.
As far as using the media from your HOB
as long as it fits you can use it. Unless you are planning on using the HOB
for another tank I would just leave it on there. If you want to remove it completely I would still let it run on your tank for about 3 weeks while you seed your new canister with bacteria.