Questions on Drip Rail Sealant Application

[Subzero]

All in effort to make the truck more water tight, I'm replacing the drip rail sealer as the stuff inside the rail was some sort of dryrot house caulk right over the cracked up original sealer. It held water under it that seeped through all the numorous holes. I scrapped all of the old filler out with a 1/4 inch srewdriver and a rubber malet to hit the back of it. I got 95% of it out and all that's left shouldn't be an issue but I can't easily remove it without messing up the paint. From what I saw before removing the sealer I thought I'd need some fiberglass filler but only a small amount of surface rust existed. I taped everything off and put POR15 inside the bottom of the rail where there was surface rust. It is now completely dry. Should I lightly sand the POR before using the new sealer? How do I make sure the new sealer is going to dry flat? Does the sealer need to go in the vertical drip rail part by the back edge of the door? Here's a link to what I'm going to be using http://www.levineautoparts.com/transtar4172.html

Thanks