A relay can do all sorts of things. Since it is a mechanical switch it can bypass an effect, switch on effect "boost", switch 2 pedals around in order, move pedals from series to parallel, switch amp channels, switch pickups, turn on Christmas tree lights, launch a cruise missile or make toast.

Once you have the Switch Witch working, you don't have to reprogram it or redesign the hardware, you just wire the relays to suit your current setup.

You can't attach a relay directly to the microcontroller, it draws too much current from the chip. So you use a transistor "driver" to switch the relay on. It's not complicated. Relays need a diode across the coil to protect the transistor.

There are 3PDT and 4PDT relays which are more expensive. You can probably attach 2 relays to one transistor driver if you have to, I haven't tried that.

GEOFEX:Relays for Switching Audio Signals

I had thought that you could do an order switcher with 1 DPDT relay, but apparently it takes 2, or a (US$7) 3PDT. See The Juggler - an Effects Order Switcher from GEOFEX. The CMOS is cheaper but it more complicated, and not true bypass.

J.D. Sleep Project you can automate:

Series / Parallel Switching with 1 DPDT: "The Parallelyzer" Project

Requires 2 DPDT relays and 2 programming switches, plus a fair bit of extra circuitry: