Alright, I'm coming back to this thread after testing it again for the Imperials. You have to give away Markarth (for Riften) and Falkreath during the negotiations, which requires that the Stormcloaks feel that you're supporting the Imperials too much because you let the Thalmor ambassador stay. Once you've finished the main quest, Tullius will, later in the civil war questline, give you missions to take back Ft. Sungard and Neugrad. You can clear out Ft. Greymoore (the one in Whiterun hold) any time, and it will be garrisoned when you come back later. The only fort I can't get them to take is Snowhawk, in Hjaalmarch, which the necromancers seem to have a death grip on.
Still need testers for the Stormcloak side

What you'll have to do is kick the Thalmor lady out of the negotiations, and exchange Riften for Markarth. The Empire should at this point ask for a minor hold, which should mean either Dawnstar or Winterhold. I've had a friend confirm that you can clear out Fort Amol at any time for them and the Stormcloaks will occupy it, and that they garrison Fort Greymoore if you clear it out after taking Whiterun.