It will be very hard, probably impossiblr to cut glass panels on assembled tank.
Dont know glass thickness, but its very hard to apply pressure and score in one motion, and there snap glass, if panel itself is not on flat and hard surface.
This way, glass where u cut is basicaly in the air....
Best way is to lay glass in hard surface, straight, with some soft cloth or similar, score glass in one motion, then lift panel, and put something few mm height underneath glass where u score, and then simply apply preasure on both sides. This work great for thinner glass, up to 6mm, for 8 and 10mm, its best to apply preasure until you see that crack is expanding along the line, then put this "plug" on oposite side and do the same, meaning you dont want to snap it completely, just to expand scoring line, when u do both sides, and line connects, then u snap it completely....
Also, angle of cutter is also important, u need to go straight and vertical as possible, if u lean cutter on one or another side, glass will not break straight, u will have to sand, also, the thicker the glass, the more carefull u need to be....
If you properly dissasemble tank and cut glass, siliconing it again is child game.....