In the winter we layer just like everyone else. Probably the most difficult part of running in a habit (especially a white one) is that if it there is mud or slush on the road our hemlines get very dirty. For that reason we tend to have a designated "running habit."
One last thing about the habit: we designed them for running. Although the skirts are long, they have 4 big pleats. Our stride is never hampered by our skirts. So, running in the habit is easy once you get used to it. Some of our sisters ride bikes in their habit. Unfortunately, that is a skill I never mastered. The skirt always gets caught in the bike chain. Maybe I should practice more.