Iechy
I just looked at my BakPak.
The side chamber you want to make into a refugium measures approx. 3"x4"x14"
That's about 168 cubic inches of volume. Not too bad.
What I also noticed is that there is around a 1" clearance at the bottom, which allows the water to move from the bubble side to the exit chamber ( biomedia side ).
There isn't much room down there for live sand. If you placed an inch of it down there you would have around 12 cubic inches or so. The problem is when you turn on the powerhead, the water entering the one side must be able to flow over to the other side and exit out the top side fitting.
I'm afraid the sand would get all stirred up, and not offer you any benefits.
I would not put sand in it at all. Just doesn't seem like there's enough room down there to mess with it.
Placing some small nuggets of live rock down in that chamber may be your best bet. As long as it doesn't restrict that 1" path that connects the two sides you'd be okay. You could certainly stack up a fair amout of live rock in there and not restrict flow.
Would certainly look unusual, but would work.
Placing some caulerpa in it would also be possible.
It's sort of a vertical refugium idea, so with only the 3"x4" area, about 12 square inches of space, lighting this will take some creative ideas. If you light it from the top with a small grow light, I'm afraid the top caulerpa would do okay, but the lower algae may not receive enought light.
You could easily light the chamber from the sides, using a 12" fluorescent bulb. You could use multiple bulbs and light it from more than one side too.
The real issue I see is keeping an eye on the caulerpa growth, and maybe dropping down to a smaller powerhead.
The Rio600 works fine when using it as a skimmer, but may be a little more flow than you'd want if you were converting this to a vertical refugium.
Maybe a Rio200 would work better - lower flowrate and all.
The last thing - as mentioned, keeping a close eye on the caulerpa growth. You'll need to harvest it often. I would imagine that if it works well, the macro algae may get pretty thick in this chamber, and if allowed to grow too thick, you could restrict the flow of the exit hole/fitting and overflow the thing.
But it would be worth trying - not too expensive if you already have the BakPak - and would be a fun experiment especially on a smaller display tank. I would not try and run it as a protein skimmer AND a refugium at the same time. One or the other.
What size is your display tank BTW ?