It doesn't really matter whether a guitar has 2 or 3 pickups. The effects loop basically interrupts the signal path just before the volume/tone controls. The signal is diverted out to the effects -(pedal board/stomp boxes)- and returns to the guitar to then be sent through the volume/tone controls and then out to the amp. The theory is that the effects always see the same signal, making it easier to replicate the sound from gig to gig, venue to venue. I essentially achieve this by always keeping my guitar's volume at 10 and using a volume pedal at the end of my effects chain. In my set up the signal does go through the tone controls first, but the effects are always seeing the same volume. It basically has the same result, but I can go cordless (as I prefer) rather than being anchored by two cords, as necessitated with the Garcia effects loop. In fact, I'm having my custom Further built without the effects loop.
Bill, tgo