I had a few holes in my sump (I took a 120g reef ready tank, removed both overflows... The bottom was drilled with 4 holes). What I did was order the proper bulkheads from BRS (I got threaded x threaded ones)... Then I went to HomeDepot and picked up some plugs from the plumbing section... I cut the bulkheads down to fit, so just the nut, rubber grommet, and flange are hanging outside of the hole / tank... I used Teflon tape on the threads (or glue if you buy the ones with a slip), and glued/taped the plug into the hole, I also glued around the edges...
I'm a bit of a perfectionist, so I took my cutting tool and made as much of it as smooth as I could... I did have an issue with 2 of the holes being a little larger, and HomeDepot not having the proper fitting plug, for that I got the threaded x slip connector, Teflon taped the threaded part, screwed it in, then I found the next size down plug and it fit inside with some wiggle room... I used pipe glue and glued it down so that the water pressure would further push it down, and filled all the wiggle room in with pipe cement...
Once installed I also went over it with some silicone just to make sure...
Yes it was a fair amount of work, but I look at it this way... if I ever decide I want to setup that 120 as a tank and not a sump anymore, all I have to do is remove the bulkheads, and all I'd really have to do is drill out the plug and poof I already have bulkheads installed for the plumbing...
