OK weld thru primer burns away. So don't think it will be perfect there. For that reason I usually don't use it. But I have no issue if someone does. I try to get into areas with something after the welding, if at all possible. You can pour a material like Master Series, into an area and let it flow. There are materials specifically made for internal areas as well. I use MS in post any place. I even coat pieces with it before I weld, similar to what you are doing.
Rosettes or plug welds . . I would never go smaller than 1/4". It would be too easy to bridge the hole without getting penetration. So either 1/4 or 5/16 is typical. With 5/16 you can really know you are penetrating before you actually fill the hole. Those welds shown look really nice, albeit a little low. Sure it creates the right look, but the strength could be a bit weak because if the thin area actually doing the holding. I treat it like an ice cream cone :) I start in the middle for the puddle, then make a circular motion to fill the hole. This is much like putting soft ice cream in a cone. At least that is how I think of it :
If anyone wants some clarification ask away.)
As Gary suggested a coarse flap disc should do it. I use them on a 4 1/2 angle grinder. Sometimes very little grinding is needed. It depends on whether you're trying to hide the weld or just leave it factory looking.
OK, so I just came back to report that attaching the first stake pocket seems to have been a success. As I do further work on this bed I'll switch back over to my own project thread, but since you guys offered up some advice on the welding I figured I'd report back on the progress.
I tested some 3M weld-thru primer and yes you can certainly weld through it, but man does it cause some splatter until you burn through it. Anyway, I did use it on the stake pocket, but I cleaned it off where I'd be welding to make life easier.
I went a bit clamp happy as you can see, but it went better than I expected. I had to squeeze the pocket a bit to pull the flanges in. Most people probably wouldn't notice, but there's not much of a gap between the stake pocket flanges and the ends of the fiberglass fenders.
I am going to grind the welds down flush or almost flush before painting.