Use a 3 pole 4 position switch for a two pickup configuration. Actually there are many ways to apply this switch. One example is the EB3 bass it uses a 3 pole 4 position rotary switch and adds some tone capacitors to filter to the desired frequencies. You can view the EB3 design here. EB-3 series #1 & #2 You can also use different caps and design a harness for guitar using the same principles. Here is a basic design of a 3 x 4 switch being used as a simple pickup switch. Options aside from each pickup you can wire parallel in/out and or series in/out you can tweak some tone by adding capacitors or choke.
This design gives you neck, neck/bridge parallel, neck/bridge series, and bridge. If you follow the positions and see what is going on with each position you can see it would be easy to ad alternatives such as split coils reverse polarity and so on.