I used a standard syringe to apply the cement. These can be gotten at most hardware stores. It allows for very precise control over the application of the cement.
I decided to make one 90 degree corner to start assembly. The reason I chose to do it this way was that the 3/8" acrylic was wide enough to easily clamp at 90 degrees and square. I think thinner acrylic may be more difficult to get square, and alternative starting points may need to be used.
Here is another good view of the first joint. It shows the pipe clamps use as well. Generally, the pipe clamps are used with stiff metal pipe, but the pipe I got for this use DID NOT FIT even though it was 3/4" pipe...kinda ticked me off since I had to cut it to get it in my car, and the hardware store won't accept any cut material in return...so I have two sections of useless metal pipe I will not be using in the aquarium. Happily, the 3/4" pvc I am planning on using in some of the tank plumbing DID fit, and worked well.