No need to clear between the base color and the stripe color unless you prefer to do it that way, some people do. When I spray lemans stripes or something like you are doing, I spray the base color, then wait approximately 2 hours (check the tech sheet for the paint system you are using for recoat times and handling times) then mask off the stripes and spray that color of base, remove masking and clear it all at one time. 3 coats clear, Let the clear dry a few days (at least one day in the sun is great) and then 600 grit it all flat to bury the stripes and 3 more coats of clear, sand and buff as normal. I cannot speak for any stencils though, as I have never used them, I always tape everything with fine line tape and lay it all out with measurements instead of the stencil kits.
Kelly