The type of weld being done honestly depends on the extent of the repairs your are going to make. If you just have a few holes I would simply cut out the bad metal and replace with either butt or lap weld.

If you have an extensive amount of repair then you probably should get a floor kit. I used an aftermarket floor kit with a transmission hump built in and it was fairly simple to cut out all of the metal in from of the seat and replace the toeboard and front floor pan. Putting in screws first helps alot to keep the metal in place.