an old maple tele? is it a fender? Anyway, you want to get the finish even, if soem areas are bare and some sealed, you may notice a difference when refinished you have many options, I would continue to sand through the sealer, then stain. If you are looking for a clear coat you can spray lacquer and buff (See finishing tutorials) or finish with a tung oil.
For the SG, if you want the grain to show through, stay away from paint. Stain it then seal it or lacquer. I read somewhere how Gibson got the deep reddish brown look for many SG's but I can't remember where I saw it.