My advice is that if it is at all possible, get your acrylic supplier to cut the material for you. Ive been building a sump/biotower and an aquarium. The sump will be made from 1/4" and the tank from 3/8". I had the acrylic shop cut the pieces for the tank, and I am cutting the pieces to make the sump. Since the sump wont be visible, it doesnt have to be perfect, just water tight. Even though Ive been very careful at cutting on my tablesaw, Im finding that it is hard to get a nice straight glueable cut. This may be due to fragments of acrylic blowing into the path of the piece Im cutting. Be sure to use a blade meant for cutting plastic, and blow off your saw after every cut.
As far as gluing goes, Im tryin different applicators out. The 1st one is a small squeeze bottle with a long needle on the top. This works well but it tends to drip on the work if Im not careful. I also bought a syringe style applicator, this seems like it will be better at least when it comes to the dripping part.