Lets see if I can clear it up a little.
The new brackets use the original factory seat pan and seat pan riser holes. Pretty sure I welded the heads of the allen-head screw to the brackets, which pretty much made them into studs.
You can put the nuts on these new studs in the normal way from under the car, through the original access holes.
As far as the original seat tracks. These are bolted fast to the seats and then the new brackets BEFORE the whole assembly is put into the car.
A hole (about 5/8" diameter) will need to be drilled into the top of the seat riser so that the front studs/nuts of the original seat bracket will have somewhere to go--it is just a clearance hole and nothing gets bolted to it. If you are moving the seat back 2" on the new brackets, then this new clearance hole will be 2" back from the original front hole.
You only need to drill one hole per seat track (just for the front stud/nut.) The rear most factory seat bracket stud will actually be behind the seat riser and will not be a concern. You will need to add a similar hole into the carpet for the stud/nut to pass through. The lower floor pan is not drilled as there is no need to access the cavity--the mod cannot be seen from under the car.
After the mod has been installed, R & R'ing the seats from the car with the is no more difficult than the original installation--actually it is the exact same procedure.
Clear as mud now??
P.S. Since I plan on replacing my carpet this month, I will add some pics to that web page showing the added hole in my seat riser, plus one few showing the assembly bolted to my seat.