I'm thinking about welding in some new sheet metal on my floor board. What would be the best way to go about doing this? I was going to cut out the old piece, fit the new piece in and butt weld it together. Im going to be welding from the inside of the car so do i need to worry about the waterproofing crap that is on the underside?

I'd flange weld for strength and yes the undercoating should be stripped back, it burns easily and stinks very-much-bad.
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'68 SS-396 1/4 stroker "54" (soon)
'99 GMC 7.4 Vortech
'01 T-Cat 1404 Hooper 2X156"
"no replacement for displacement"
-2 Below Custom Automotive
Fbks, AK.

If you flange weld, you will need to weld both sides, since the overlap will be very prone to corrosion. A butt weld will do fine, unless this is an area where there is a seat mount or near a body mount. In that case, I'd go for the extra strength of a flange or overlap weld.
Underneath, just be sure to grind it smooth and paint it to match the rest of the area.

The section that i am working on is right where you put your feet. The previous owner has metal that is pop riveted to the floor with some sort of sealer around it. I thought about doing the flang style being easier but thought about the risk of water getting between the pieces. Considering i only drive it about 500 miles a year and only on dry days i guess it would not matter.
Thanks for the help.