Do some google searches on "biocube mods" and see how other reefers modded theirs. There are so many options. Click my 29g in my sig for some other ideas too.

It's up to you and what you think will work best for you and your setup. I ran a 14g biocube stock before and it was great. I also ran an 8g with no media and only a fuge and that was great too. My current biocube is loaded with mods and it's running great as well.

Typically any section that does not have a pump in it will work well for live rock. A fuge section would go where the intake would be..followed by a bubble trap. I have found it helpful.. to add something to the bottom to keep whatever you put in (rock or macro) from settling at the bottom or moving from one chamber to the next. A usefull item would be something that has holes and is water safe such as a plastic container with holes in it or egg crate ziptied together to make a box. Make sense?