Marie, one thing that you may want to consider when adding glass baffles to a glass 40 breeder is to have the bottom corners of a few baffles ground. What i mean by this is, when you have a baffle right on the floor of an acrylic tank, all of the corners meet nice and flush. But with a glass tank you have that whole silicone bead to get in the way. It doesn't cost that much more to have done, but when you order glass just ask for a 1/2" radius to be ground on the corners that will be sitting on the bottom of the 40 breeder.
Basically you will want to make your skimmer chamber a pretty snug fit around your skimmer. But large enough to maneuver it about. I find that drawing in your baffles on the outside of the tank is helpful. Then go to the opposite side of the 40b and size up your return chamber. If you have an ATO you can make this section much much smaller which will add a great deal of size to your fuge. You can pretty much safely about double the size of your fuge if you run an ato
Any idea what model of skimmer you will be using? Return pump? An ATO?