I just finished patching up some rust in my trunk. What kind of sealer/calking should I use to fill in gaps? What is the white stuff that came in the trunk from the factory?

gaps? I would use seam sealer along the seams but it will not do a lot for gaps

What I mean is that I want something to fill in any pits in my welded patches. I had to do hundreds of tacks rather than a nice bead, so there are little divets here and there. I dont want to have any little spots for water to pool, so I want to put a layer of calking or something over my welds.

oh then use seam seeler , you can buy it at autozone I would prep and paint the welded area to keep it from rusting then cover it with seam sealer ,

Great, thanks for the advice.

I like to brush primer on areas like this to work it down into the cracks. I use PPG epoxy primer, but you can use Rustoleum "rusty metal primer" in a spray can. Load it up, brush it in, & let it dry. Get the autobody seam sealer in a caulking tube: you can use a towel to brush over it to look factory if you like, or just smooth it out with your fingers. After it drys prime the area again. Make sure you do both sides to prevent rust.
HTH,
~ Paul
aka "Tha Driver"

Custom Fiberglass Parts