Filler coats on an open bay wing can be brushed or sprayed.  I usually brush on 3~4 coats, and then spray a final coat or two.

Dont try any sanding of open bays untill the weave of covering is completely filled, and you have added several extra coats on just the capstrips.  
Actually I find it comes out smoother if you put the extra capstrip coats on first and then the filler coats to the whole wing.