I try to play to some extent in real time. I avoid time warping unless it's just for a few minutes where I can't do much else. Otherwise, when I get to the waiting phase in a mission, I switch over to another concurrent mission.
Sometimes this causes problems when you get unlucky and have multiple maneuvers line up at the same time. Then you have to juggle which ones can be delayed, like a mid-course correction, and which ones are critical like crew re-entry.
My goal is to see how much I can get done in x calendar years.