How do I setup IntelliTouch with IntelliFlo?

I have the IntelliTouch i7 with the IntelliChlor unit. I recently added the IntelliFlow pump (replaceing a 2sp Whisperflow). I guess I don't have the Intelli-gence to get this setup right.
I "had" my IntelliTouch setup to run the pump from 7AM to 11AM, then run the pool suction cleaner from 11AM to 2PM, then go back to pump mode from 2PM to 4PM. Then I added the IntelliFlow VS.
Now with the IntellFlow pump, my IntelliTouch program does not give me the option to have a second pump cycle. It doesn't seem like anything works at the time it is scheduled in the IntelliTouch. Also the IntelliTouch starts up in the middle of night (ramps up a couple of speeds) then shuts off. Seems like this happens randomly. By the way, I can see the IntelliFlow and set parameters for it via the IntelliTouch (they are communicating).
1) My IntelliFlow is set for 20K gallon pool, 3 turn overs a day, 3 cycles a day.
2) I have the Ext. Control Programs (1 to 4) Disabled.
3) I have the Features (1 to 9 and M.O.) Disabled.
4) I have the Filter Modes (Start and Stop Cycles) for cycle 1, 2, and 3, set to the same times as I scheduled the IntelliTouch for - but I don't think I should have to set this. This was my latest attempt from this weekend - still not sure if this is doing anything.
I thought the IntelliTouch was supposed to control the IntelliFlow. Do I even need to set the Filter Start and Stop Cycles?
Thanks.