Thank you for contacting us. The finer sponge goes on the bottom and the other sponge goes on the top. In terms of how much media, we usually recommend fill the chamber 3/4 of the way.
If you go to the product page, the second picture is an assembly diagram that shows you how to connect both chambers and run all the lines:
http://www.coralvue.com/reef-octopus-sro-cr5000d-calcium-reactor
The link is for the CR5000D but it is the same as the CR3000D. The only difference is the size of the unit.
Let me know if you have any other questions.