The "BEST" way is to cut out the floorpan and weld in another.
Next best is to cut out around the hole and weld in a patch.
What you want to take note of in particular is how thin the metal has gotten around the hole. In general, rust doesn't just form in one tiny spot, at least not enough to make a hole. By the time a hole has formed, usually a large portion of surrounding metal has been eaten away and thinned considerably.
Cut out as much of the offending metal as possible, until you are satisfied with the thickness. Even if you are satisfied with the thicknedd, if there is surface rust, get rid of it. Grind it, wire wheel it, doesn't matter, just make sure its gone.
If you dont have a welder and don't see it buying/borrowing one as an option, consider cutting your patch 1/2 to 1 inch larger than the hole on each side, and JB weld the thing on there. No, this isn't ideal, but since the floor isn't structural (not a unibody) then all it really has to do is keep you from doing a Fred Flinstone impression. Buy some seam sealer and seal your edges.
I don't know if Herculiner is indicated for use over bare metal, so I'd like to see it primed first. An epoxy primer is best, but lets be honest, if you aren't welding a patch in, its an imperfect repair anyway. That said, you can probably get away with an off the shelf automotive primer (self-etch or other).
Just make sure your metal patch is slightly scuffed (if you dont use the etch primer) and degreased (can use acetone, laquer thinner or similar)
Good luck to you.