Autopilot application question

I'm looking at converting over to a swg and leaning towards the Autopilot. My questions involve if it is the right choice for my configuration. Pool is setup with 2 pumps running off of an Intermatic dual controller, uses a seperate output for the primary and booster pump.

Looking at the Autopilot unit manual it doesn't appear to have the capability to run both pumps independently. If I understand it correctly I could run the primary off of the Autopilot and leave the booster pump on the Intermatic, or I can slave the Autopilot off of the primary control of the Intermatic?

Neither seems like the ideal method.

Other questions is...the booster pump is plumbed into the return line to the pool, it is located such that it would be right after the Autopilot. Does this configuration present a problem with the functioning of the unit?

Any help would be greatly appreciated and if there is a better unit that may fit my setup better I would be glad to hear about it.

Thanks in advance.

Ideally, connect the Pool Pilot to your existing Intermatic, as you are correct, it cannot program the main and booster pumps.
The location of the booster pump may be affected by the Pool Pilot's chlorination and should be installed before the manifold assembly. If your booster pump has no metals (think shaft seal, impeller, diffuser screws, etc), then the Pool Pilot would have little affect on your booster pump.