i got the good 3/4" plywood from a local plywood supplier. it's not "cabinet grade" but the material has a few sections filled in. Since it's not for appearance it's perfect and even came oversized by an inch which allowed me to keep seams to a minimum (6' x 10' bed). I only sized it per the directions so i do have a gap of a couple of inches around the perimeter. My machine came with the vac hold-down system. Silicone was used to attach the air layer to the plywood base and then also used silicone to attach the spoil board (LDF). On a side note, I always put a couple of screws in the corners of the sheet I'm cutting as an extra precaution keep it from moving at all. i sometimes cut 1/8" aluminum and those sheets are too expensive to waste.
As far as leaving a gap, IIRC the instructions specified exact sizes for everything. That's up to you. i don't store anything under the machine that will be hurt by some wood/metal dust.
I will second Harbor Sales (Baltimore area) for sheet goods, but I got my base plywood layer from Fessenden Hall in NJ. Harbor will deliver a single sheet of coroplast (that cheap corrugated plastic you see on lawn signs) for a regular customer without delivery charges. They have started to add a couple of bucks for a fuel surcharge.