Big Bean fan...the glass tank I just got has that, haven't fired it up yet.
As far as acrylic goes, IMO, a hole will weaken a tank much less than a slot. A slot basically disconnects the panel from the top eurobrace, and thus must have additional (structural) bracing added to compensate.
Considering that you can put a few holes along the back and space them apart adequately without weakening the tank that much, I would go that route.
The reason I asked if the tank was new or used is that a used tank has material that has already been stressed during use. This means that you will have to make sure the back panel is nice and flat when joining the box, and this might be difficult. The other option is to just make boxes and hold them on with bulkheads through the holes. In that case, I would make both out of 3/8" General Purpose Plexiglas, should be nice and solid.
Floyd, I'm almost ready to drill the holes for my 2" bulkheads. Going with the Beananimal overfkow. What would you consider adequate spacing considering 3/4" acrylic thickness on the back panel. Thanks again for all your help. If be at a standstill without it.