Do torque boxes first. I assume you are replacing the toe boards, also? Do torque boxes, then toe boards, then floor. Get the 2 piece, more expensive torque boxes. I bought the pre-assembled pieces and the flanges and such seem to be bent/cut to replace them as stand alone repairs/upgrades(in the case of 65-68). To be more exact, the flange that welds over top of the frame rail is cut out because you wouldn't be able to install the torque box unless you are cutting out the toe boards as well. Also, I think(?) the flange against the rocker is bent down instead of up, which also aids in installation because you would not be able to get to it if it were bent up in cases where the toe boards are not being cut out.
I wish i had known this before I bought the parts. The suppliers do not detail what the differences are. It all depends on how extensive your repairs are.