Depending on the car, you may not have to cut anything. My floor enclosures consist of 4 pieces of mdf, no bottom, massively caulked to the floorboards. If need be, I can remove the enclosures with a carpet knife and some elbow grease. I did cut the carpet for the speakers and there is a super heavy duty Black ABS speaker grill on it. That thing has paid for itself a week after the install. For competition, the ABS will be replaced with a standard grill.
The enclosures do not interfere with my shifting. I can't feel them there unless I crook my legs back during Cruise Control runs.
By the way, Speaker Works installed my first system.
BigRed has actually cut into his floorboards but he has a Monster Truck and those cabins have air space behind them. It makes for a really nice fitment.
If your car can handle floor enclosures or floor mounting, it may be a way to go. The location makes it way easier to handle vibrations/buzzing/rattling.
Good luck in whatever you eventually go with...