I've had good results with staining before or after sanding, and yes, you can paint over the stain. I think unstained caps look better when I've just sealed them in clear first, although that may not even be necessary.
Use some masking tape around the shaft where you want the cap to end and just stain to that, remove tape, sand with 0000 steel wool and clear seal the whole shaft. Let dry and paint and crest the unstained caps how ya want 'em, and add a couple more coats of clear finish over all (make sure all this is compatible) and finish 'em up when they dry. Then go shoot!