How do you sync the output of Zone 1 and Zone 2.

The only way to have the 2 zones in sync is most likely to have the amplified with identical connections and amps. You need a multizone pre-amp with matched amps for each zone.
Even then, you won't get "exact" unless you are careful with matching interconnects and speaker wire lengths.
Finally, you will probably want to use matching speakers too.
Then, you still have to worry about the delay with you running from room to room to compare...

When I was using a B&K processor both zones were in sync. The two rooms are about 35 feet about. Could it be that I am now using the internal amps from the the Onkyo for the Main room and external amps for zone 2, when before I was using external amps for both? What if I used the Onkyo"s internal amps for both zones?

Should work much better using all internal. The other option is using the Marantz (better amps) for both zones with an a/b speaker selector?

I am also using a Sonance DAB 1 for multi room systems. I have three other zones. How does this effect the sync? Only two of the five zones are close enough for me to care about the audio sync'ing.

I'm using a Niles 8 pair impedance matching selector for my house. 5 zones off 1 amp and main zone off the Denon 395 multi-room receiver. I honestly never notice any delays from room to room. This is thousands of feet of runs.