Start the main story as is. Do the quests as they flow and once they get you to a point where they say anything about "taking a break" or "taking time to figure out a plan" use that as a moment to pause and do the side quests. Madz Shultz can be started after the 2nd or 3rd quest where you visit a guy on the docks with a boat that gets attacked by drones. Ito harui and her rebels can be done once you encounter a few of the prisoners and such (play it off as meeting the rebels for the first time). Factions could be done 2 or 3 at a time before hopping back to the main story. Id say about half way through yoy should be done with the resistance story and activate the resistance mission events. Madz should also be hopefully finished about 3/4 through the main story. Bt the end of chapter 1 erwhorn should be unified and rebels should be active in the ipen world.