For raised rivets, glue drops are most common. A small drop of glue makes a dome shaped rivet that can be painted over. For flush rivets, the best way I know of is to melt them into the primer coat. Mount a 1/16" OD brass tube to a soldering iron (I used the Top Flite Trim Iron). When you touch the tip to the primer, it'll melt a small ring. Give it a light sanding, then you're ready for the color coat of paint, then weathering.

Scott