Interior Carpet Question

[Ewr101]

After finding my front driver and passenger seats held down with less than a quarter of the required bolts and the seat belts held in with undersized bolts that you could wiggle out by hand, I went to the hardware store and picked up all new, correctly sized, Grade 8 bolts for all the seating and seat belts front and rear. In the process of replacing them all I found that there were two layers of carpeting, fabric heat/noise deadening material and bedliner sprayed in. All this made it difficult to get everything tightened down correctly. My question is should the carpeting and other material be cut back so seat brackets are able to bolt directly to the body? For safety sake, that's what I did, I cut enough of it away so they tighten down directly to the floor, no carpet in between. How did it come from the factory? I'll be taking out ALL the carpet at some point and would like to install the new carpet like the factory would have...