Michael,
An important starting point is to decide whether you want just 1 bucket or more. You can build a very nice bubbler bucket without the need for circulation. But for multiples the circulation factor makes the initial build more complicated?..but the maintenance from that point on? simplified.
For a single bucket, take the time to look at the Weezard??s gallery??he??s worked simplicity to the n??th degree.

I guess the reason I was so confused was looking at the instructions here: Lets Build a Bubble Bucket *Step by Step* - Grasscity.com Forums all kinds of pvc fittings, multiple holes drilled, are these all necessary?

All that is unnecessary for a single bucket.

and how do you know how high to have the water

LOC NAR did that one above.

I guess its okay for some of the roots to stay completely dry?

Nothing is going to survive ??completely dry?. That??s one of the reasons for the bubbles, to aerate the solution and to splash enough moisture onto the roots to keep them from drying out.

Again?..luck to you.

HMR