There's a lot of ways to go about it, but the most common way I've seen around the local area is to just build everything off a skid in the back of the truck. It's WAY easier than trying to bolt everything down to the stock truck bed. I'd recommend you bolt the skid down though.
My two cents, make sure you can get at the machine and have sufficient room to move around in the back. IMO, if you have the space left over, I'd suggest using a greenlee box as a toolbox (You can cram whatever you need in there!), though topside toolboxes will leave more room in the truck for bottles etc. Biggest thing is to keep everything neat and organized. You'll save yourself a hell of a headache!