Steve,
Your rough cut piece must allow for a finish cut of the profile, such that, if the piece when placed on the table is somewhat angled releative to X or Y axis, the profile can still cut within the roughed stock. I would know a dimension from one of the points to the program origin. Then you just place the rough piece on the table,
move to one point, ref all axis, now move the distance to the origin, rereference the machine, and your ready to go.
For a quick set up you may want to use set up a laser which will give you a visual for aligning the piece. Only a couple of bucks to do and woud save time.
Need to consider how your going to hold the piece down as Gerry mentioned.
RICH