What should I use?
 

There was/is some rust underneath the fender at the seam. I did some sanding and grinding to get most of the rust removed but the sanding removed some of the sealant that is used at each seam.

What is best to use to fill that back in?

You just want to replace the sealant? Prime with a rust preventative paint (POR-15 is best but very expensive and overkill for a small spot, Zero Rust is a next best step) and then heat to the auto parts store and buy "seam sealer".

Awesome, "seam sealer," too obvious. Ha! Thanks a lot. I primed over the spot yesterday, gonna sand it and grind away again today. I'm using rustoleum auto primer, you think that will be sufficient?

I don't know about that product specifically. But most primers contain a lot of talc and must be topcoated or they will absorb moisture and cause rust.

pm'ed ya.