M,
I assume, based upon your initial post, that they only plumbed one hole and that the other hole has nothing going to it.. The hole with the pipe going back to the equipment pad must be left open, while the hole with no pipe must be capped off.
I missed that the hole is plugged from the bottom.. That would work, but the hole will soon fill with junk. I would also cap it off from the top.
Thanks,
Jim R.