Did this unit not come with some sort of instructions? How do you have it wired now? Do you know the make/model of this thing?
Ordinarily, I would suspect that this unit would get wired to a switch so that it was able to be bypassed for a normal sound. You mentioned a toggle switch on your guitar. What is it doing currently?
Also, the usual deal here would be to have a TRS jack replacing the std. output jack on the guitar, so that the battery is disconnected unless a guitar cable is plugged into the jack. This is wired just like a pedal is wired, to save battery life.
So, for now, I've got more questions than answers . . .sorry!