mount it so you can get to the controls without climbing up on the truck.
some also suspend unit over floor so you can load steel under.
lots of room for personal preferance on this.
it all depends on what type of work you will be doing.
a pipeliner will have a different rig from the man installing dock bumpers.

edfritsch,
We used to regularly mount Lincoln AS400's on trucks usually for pipeline work.We used hard rubber strips to mount welders on.Also with your mounting bolts either drill thru deck or weld bolts on top.If drilling thru the deck tack weld bolts underneath tray and it makes it much easier to remove welder without climbing underneath truck.
As supermechanic has said you need to be able to access controls from the ground.We used to mount welder across the deck as close to the cab as possible (remember to face welder so that you can still get the door open to check/fill oil)and as near to the edge as possible.If you have the welder all the way to one side it will unbalance the truck so what we did was mounted our oxy/acetylene set on the other side to even out the weight.
Some people mount their welders lengthwise on the deck with the controls accessed from the back of the truck tray.
It is pretty much dependant on type of vehicle, type of terrain and personal preference,
Hope this helps,
Regards,
Shane