they say to leave around 1/8" of room on each side of the glass when making baffles. i just did mine and it worked fine, just apply a 1/4" bead of silicone and make sure the silicone makes it between the glass, worked for me. then use your finger (lick it first) to gently pressed the silicone into a wedge.
for the external overflow box, i would assume to make it snug by applying the silicone and then pressing the glass firm on it, then do the same as if you were doing the baffle.