Drain to refugium?

[Mugg1977]

I have split my drain to go to both the skimmer compartment and the refugium of my sump (center return section). Flow is controlled to both sections by ball-valves, and isolated by unions. My question is regarding the drain to the refugium. I have built a bubble tower to hold live rock rubble. Should I run the drain to the bottom of the tower, with a tee and holes drilled in the pipe below the water surface, or should I cut the pipe off just above the water surface?