Always best to sand body and neck separately. So much easier and with less risk of hitting things when re-positioning.

If the back of the neck is going to be left natural, then make sure you thoroughly tape up all around the sides of the headstock. It's very easy to get any stain (wax or liquid) running over the edge and spoiling a natural finish. I'd suggest getting hold of some Frog decorators tape, as that seals at the edges better than the normal masking tape.

You don't need to treat the ebony board as such, though occasionally applying some lemon oil helps to stop the board from drying up. It will also make the board look darker. You can apply wax to the board, it's not going to harm it, though this is more often used on otherwise untreated maple fretboards.

You've got a basswood body and a maple neck/headstock, so you'll probably find that the stain comes out a bit lighter on the maple headstock, so you might need to apply more on it than the body. Certainly don't sand finer than 220 grit on the headstock face or the maple will absorb very little stain.

How do you plan to finish the rest of the guitar once the stain is on e.g. Tru-Oil, wipe-on clear poly, clear acrylic spray etc? Whatever you plan to put on over the body, you can put on the back of the neck. Or you can do the back of the neck with something very different e.g Danish Oil. You don't want to leave it totally bare as it will a) get very dirty very quickly and b) be more susceptible to humidity changes and so may need the truss rod adjusted more often.