StewMac NitroCellulose Fininshing Schedule

So Im building a guitar with an alder body and mahogany neck. Now according to this schedule I need to use grain filler on the neck and then I plan on staining both body and neck cherry red. So heres where my question is if i just stop there and only stain then whats the difference between sealing and applying clear coat if theres no color coat involved? I only ask because the products they suggest for both are the same.

Now say I want to paint a symbol or something like that on the guitar.. and i will be painting the face of the head stock black at least. Where does that fit in? just the color coats part?