Thanks, fishyboy. I'll only be doing one layer of screening because if a fish can get past what I have in mind, well...they won't be able to. It'll go right up to the lid height, confident nothing will get past (based on experience).
the_deeb - the height of the pass-through holes is the recommended method based on the ReefCentral folks' experience, although I agree, intuitively it seems better to keep them submerged. I believe the reason has something to do with maintaining turbulence (not whitewater rapids) around the drains to reduce the chances of a vortex forming...don't quote me on that.
Further, the reason for the number of holes is simple. I have a 65mm holesaw, and the maximum number of 65mm holes I can fit across that width of glass is 3. Don't forget...65mm is almost 3". Rather large holes.