Thanks for reaching out, this is Lucas with Rachio support -- happy to help clarify.
In short, the "total watering time" should be a sum of all zones, within any given schedule, per run. Without further insight into your scheduling specifics, I'm afraid I can't offer much more explanation on what you're seeing.
Any chance you could include some screenshots of where you're seeing this? Also, it would help if we knew a bit more about your schedule type and settings (i.e. - WAN schedule with Smart Cycle enabled?)
The picture below, for example, is from my Backyard schedule:
Two zones contained, therein: