Well, I'll be building my own cage soon, and I spoke with the allmighty Rich from Reptile Basics on just that thing.

He suggested (and does in his own cages) placing the flexwatt/mat down on the inside floor, then placing a sheet of plexi or glass over the whole floor and sealing it around the edges. A 'probe channel' is then cut in the original floor under the tape to run the t-stat probe. If tape ever needs replacing, just slice the silicon seal and lift the plexi.