If the tank has a plastic rim on the bottom, you may need to redo the bottom pane as it was for the rim to fit properly again. If there is no rim then you could do it either way. How big is the piece of glass your getting? $68 sounds expensive too, but then I haven't priced out glass in quite awhile.

The bottom has a plastic rim, but if i put the sides ontop of the bottom i figured i'd just leave it out, the glass is 48" X 16" X 3/8"

If you go without the plastic rim, make sure you use a piece of styrofoam under the tank to prevent pressure points from breaking the new glass bottom.