Maybe its just assumed, but make sure you get waterPROOF silicone. I already knew this when I went to HD to get it, but I took 'waterproof seal' to mean 'waterproof'. Yeah, my baffles stayed in place for a few hours before the silicone returned to its original (wet) state. I can laugh about it now, lol.
You can do the bubble trap gluing a couple of ways. The first time, I glued the first baffle in place, and let it set. At the same time, I put a small horizontal bead of silicone at the height I wanted the middle baffle to be lifted to. So when I went to put the second (middle) baffle in, I just set it on top of the 1/2" horizontal bead and that kept it sitting at the right height until it set. The second time I had to do this, (read above about non-waterproof silicone) I just laid my tape measure on its side, then glued that middle baffle in place. For the third baffle, I drew a line on the outside of the sump where I wanted the baffle to be. Then I ran a bead of silicone up the side of the inside wall like the baffle was really there. I set the baffle in the sump, then pushed it up against the bead of silicone, then put another bead down the other side. The reason I did it that way was I didnt have enough glue to hold the baffle in place when I added water to the system. The outside bubble baffles have to hold all the water back on each side. In other words, I had my refugium pushing on the bubble trap from one side, and the reservoir pushing on the other side. So the outside bubble baffles have to be really sturdy. The second time I made mine, I put some lengthwise supports between the baffles so that the water pushes on all three bubble baffles at once.