Is "agitated" loud, or tantrums or violent or what?
I honestly find that overall, good general parenting and communication skills always help.
I also found (but I don't know if your son is like this) that it is especially important to be predictable and consistent (once again something that is good for all kids, anyway) and to give ample warning and adjustment time with any changes. One thing in common to most kids on the spectrum is that they have trouble switching gears. If you suspect your son's father is on the spectrum, you might have to be very clear with him like, "15 minutes before it's time to leave, you'll need to tell our son you are leaving and tell him what he needs to do to get ready one step at a time".
Actually write down important routines for your son's Dad so he knows.
As for "not listening" make sure Dad is aware if he's been heard. Make sure he knows to walk right up to your son and state exactly what he wants, and have him ask a simple question to see if it is understood. Once again, this is good for all kids, but a lot of kids on the spectrum get so caught up in what they are doing that they may not register verbal instructions. If the Dad might be on the spectrum and wasn't explicitly helped with social skills or communication, he might not naturally notice if your son actually heard and acknowledged instructions.
Other things that helped in our family (especially if not the usual person is with your son) was actually posting rules on the fridge. Make sure you and the Dad are on the same page, because two sets of rules could be really frustrating.
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