Find the center point of where the woofer cutout will be and mark it on your panel. Then take a ruler or straightedge or board and attach one end of it with a nail or screw exactly on your center mark. Next, attach a pencil to the opposite end of your ruler (or board or whatever) at the half diameter measurement and carefully turn the whole thing in a circle while drawing your mark.
As far as flush mounting, you'll need a router for that unless you're planning to cut different sized holes on two or more baffle panels and then glue them all up together. With the heavy driver, it won't be easy taking it out again later but if you're careful, you can do it.
When you set it in the first time, put some large zip-ties through a couple of opposing mounting holes to use as "handles". This will help you set the driver down into the baffle without you losing a finger.