[ckwatson]

The sump I am getting only has 2 chambers in it one for the skimmer and heater and pump ect. and one with bio balls. If they are so bad could i replace them with live rock and move all my equipment to that side and just leave the pump in the return and put a deep sand bed and use it as a refugium. and if that is the case would having the water run over the rock work or does it have to be submerged to do what it needs to do?

[alwmalon4]

If you have the water run over the rock work then it is essentially the same as having the bio balls. What you need is anaerobic bacteria which means that you need to fully submerge the rock that way the bacteria can consume those nitrates and convert them into nitrogen.
The reason bio balls can get bad is because they do too good of a job breaking down organics into nitrates... thus creating a nitrate problem. If you have a FO tank they (the bio balls) can be useful because fish produce a lot of waste and can tolerate moderate levels of nitrates. In a reef system, nitrates are bad because a lot of corals are sensitive to even very low levels of nitrates.
It never hurts to have more LR for more of natural biological filtration, so IMO you should put some LR in the 1st chamber and submerge the rock completely. The rock will also help to diffuse any micro bubbles you will have from your overflow and/or skimmer.

[ckwatson]

can you put the return pump in the refugium or would it be better to alter the sump. maybe put a small chamber in one of the corners of the refugium? I think the sump i am getting is acrylic could i use lexan and just silicon it in place?

[alwmalon4]

As far as I know silicon does not adhere to acrylic but it does adhere to glass. There are good plastic adhesives out there that you can get for a reasonable price at Home Depot. I would put the return pump in its own chamber within the sump because you do not want any sand or stray pieces of macro algae to get in the pump because both of those things can do some damage.
If you are interested I can show you how I built my sump/fuge. I used pressure locking baffles. I did not have to use any glue. Instead, I used weather stripping to lock the baffles in place. Here is the website I got the idea from...baffles