I've spent a lot of time trying to research this here and through Google. Basically I'm trying to do a mod to a guitar that is similar in concept to the varitone. I have an On/On switch and a .047 capacitor and this is how I want it to go: I want to use the switch so that in one position the neck pickup signal bypasses and goes directly to the rest of the electronics, and then in the other position, the neck pickup gets wired in series with the capacitor which then goes to the rest of the electronics. I have absolutely no idea how to wire this. Can someone help me out?

You need to run the output from the pickup to the center of the switch. One of the poles from the switch will then be routed straight to the electronics. The other pole will have the capacitor soldered to it, then the other lead from the capacitor will go to the electronics. Now, when you flip the switch, you either have the pickup routing to the electronics, or in the other position, the capacitor in series.
in fac t if you solder the pickup output to the middle, and the capacitor to bot outside lugs (one leg each side) and the the rest of the electronics to one side it saves having the other side of the cap loose
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Good luck with your project. Honestly, you can do it either way. There really is no wrong way to do it - just whichever method works out best for you.
Thanks. When I finish I will make a thread about it and post photos. I think people here will enjoy it because its pretty unique.