For these quests you must choose one faction to be loyal to. As you follow the main quest arc for a single faction, the quests for the other factions (with the exception of Independent/Yes Man quests) will fail as you gain infamy for siding against them when you progress through the quests for whichever faction you side with. The point at which you fail the other factions' quests varies depending on your actions and quests already completed. Once you side with a faction you can change to another faction's quest arc, only if you have not progressed down the preceding faction's quests to the point that you fail the other quest arcs from gaining infamy.