I would just start separate activities so the device knows what it is tracking. I have the fenix 3 and break up my activities if I think they are different enough.

I'd like to plan some run/stair/run workouts on my fenix 2 and I'm wondering what settings I should use for the activity.

I plan to run 1-2km; do 2-3x300 outdoor stairs, and then run back. Some say that "indoor run" is most effective for stairs, and some have had had luck with simply "run." Or, should I make the workout two separate activities? 

I ask because fenix 2 has a VO2Max feature which tracks your output (with a HR monitor) as you run, and I'm afraid that introducing a stair workout in the middle of a run will throw it off. Any feedback would be appreciated!  

Stair Workouts and Garmin (Fenix 2)