tWelcome to the group..take another minute and fill out your profile so we know what part of the USA you are in..To start with the water on your floor probably came from a cowl or winshield leak..pour alot of water down your cowl..vents area just behind the windshield and then look to see if isn't leaking inside at the fireewall, where your put your feet area. If so it won't do much good to seal the floor..where will it get out?..and you'll just have a soggy mess from now on.
If by chance it's just from years of wet shoes and spilt sodas do not use bondo..you are better off with something as common as silicone caaulking or a steep better the small fiberglass repair kit that is at your local auto store. Once again put alot effort in determining if you have a leak first.
If you can get the underside clean enough hit it with some Rustolem brand type primer and paint. Most of the undercoating products might get a little wild trying to apply without car on stands. It really comes blasting out of the cans heavy.
The silicome caulk will work for the seams but the good stuff is true seam sealer for autos that maybe the parts store has or for sure and car paint supply store will...