Dig into it and find all the cancer, its what you dont see that will haunt you.
Then you can decide how to progress. If its just the floor pan, fairly quick and easy to cut out and replace, then when its welded in (or whatever method you choose) treat it with paint or a good sealer. POR15 is great to treat even rusty areas, but its kind of expensive. Another could be truck bed liner, but just dont leave it as raw metal.