Get the floor prepped for the install and lay down some plumbers putty, silly puddy, or bit-o-honey in the general area where the bolt hole will go. Lay the stealthbox in place and firmly press down. Pull the stealthbox out and the indentation in your medium of choice will mark the exact spot you need to drill. I've done my last two like that with perfect results. The first stealthbox I installed for a friend was with the included cardboard template from JL. I might as well have been for another car it was so off.
Don't forget to cover the hardware under the car with some type of underbody spray or treatment.