Without pics it's hard to imagine what you are dealing with, but I think I may understand. For the stand, as long as your only cutting through the skin you should be fine. It doesn't add a ton of structural support. Just stay a few inches away from corners and edges to keep the risk of cracking the wood down. I don't know if side holes are going to be a pain for you... The big thing is having PVC on the inside do a ninety degree bend straight toward the surface and then the top of the pipe= your water level. You will need that for a sump otherwise you may drain the whole tank in a power outage. I hope this helps a little.