You won't sand the glue spots off without sanding through the veneer. The veneer is 0.6mm thick.
There isn't any need to sand the veneer except for a very light 'drag sand' (as StewMac call it), where you lightly run some fine grit paper (say P800 or P1000) across the surface using no real pressure at all, to dislodge any loose grain fibres. You'll probably want to do the same after applying the stain, as water or water-based stains will raise the grain a bit, making the surface feel rough.
The main purpose of sanding is to remove any tooling marks and get the flat surfaces as flat as possible but this really is mainly applicable to solid bodied guitars where they are machined out of solid blocks of wood. Hollow bodies ones made from bent/pressed ply don't have these marks and have a fair veneer face on the outside.
The neck and headstock will probably need sanding, but not too much. And keep to P180 grit as the finest grit you use if you can before staining. Too fine a grit and you close the wood surface up and stain take-up becomes patchy.
You probably haven't decided what to use as a finish yet, but in general, you'd get the really smooth finish on your clear coats.