Question
The only zone that works on the timer is zone 6.
have any idea how get zones 1-5 to work on the timer?

Answer
Hey Dave, I would suspect that the wiring is either not hooked up properly, or the wire is cut somewhere. Your question is a little vague. Normally if 5 zones don't work, (and they worked before?) then normally not all 5 valves would go bad at the same time, but the common wire, if it was disconnected or cut, would account for 5 valves not operating. Good luck and have a great day.