Ray, here's my thoughts (collected from reading lots of other discussions on this):
1. Top mount - probably most common. Some people say the downside to this is that particles that get trapped in the filter (above your model) can get dislodged and fall into your paint. It also seems counter intuitive to try to pull paint particles against gravity...
2. Back/side mount - creates a cross draft of flow across the surface of the model.
3. Bottom mount - creates a 'down draft' that uses gravity. I built mine this way, but I have no idea whether or not it's really better than the others or not.
I don't really know if it matters all that much. The biggest thing I can see is to get the right sized fan. Too small won't clear the fumes/particles fast enough. Too much will draw too much outside air/dust into the booth.
PS. I built my booth out of heavy corrugated plastic (looks like cardboard, but is actually white plastic) glued together with a hot glue gun. Very cheap and the end result works quite well. Send me an email if you'd like more info...
M.