As I recall you were going to bind your guitar, I assume with plastic. That should provide a good interface between the stained portion and the "painted" part - you can mask and scrape at the binding. When you say "spray paint" - exactly what product to you plan to use? What will be the solvent in your stain (alcohol, water, or something else)? Do you plan to shoot something over the stained part (clear maybe) - if so what? You may want to seal the stained portion with shellac or some other sealer (with nitro I might use vinyl sealer) to keep it from bleeding into other areas.
If it were my guitar I would probably proceed as follows: Prep the entire guitar. Mask the sides including the binding to the edge. I don't try to mask the thin part of the binding, normally you can scrape that better than you can mask it. Apply the stain to the wood. When I was satisfied spray a couple of coats of clear sealer over the top.
Pull the masking tape and scrape any stain from the binding. Mask the sides of the binding again, this time stopping at the side to binding line, fold the masking tape over the top. Mask the top. Shoot your color on the back and sides. Pull the tape and scrape any little bits where color got on the binding. Take all the masking off the guitar and shoot compatible clear over everything. You are going to have some edges where you masked and scraped, you want the clear to blend all of this together. Let it cure and do the final sanding and buffing.
Like any finishing question, one of the best ways to answer it is to experiment on some scrap.
This guitar had stain applied to both the top and back/sides, then some color mixed with the finish. I masked the binding but as you can see, it needed scraping after the color was applied. It also has bound f-holes, I masked the insides of the body but didn't even try to mask the binding itself - just scraped it back before shooting the clear.