The entire activity/exercise/health tracking experience across the Watch and the iPhone is an INCREDIBLY BROKEN user experience. It is very frustrating, since Apple now has two very different paradigms and they don't stay in sync across the devices.
I really got used to using the dashboard in the health app to track the totality of my activity and other vital stats. It has done a great job over the last year tracking steps, stairs, etc. Now I have the watch and all of a sudden I have the activity tracker. Although there is an app on the phone and on my watch for it, I only get "credit" when the activity happened, while wearing the watch.
My watch has a nice leather band, so I still continue to go for long runs with my phone, come home, and then put on the watch. I went for a 5 mile run this morning, climbed 500 stairs, while running, and by noon the activity tracker (watch and phone) says I've done jack all day. The Health app is perfectly clear in the assessment of activity (60 flights of stairs, steps, etc), but the activity app on both devices is a big self esteem downer.
Apple needs to figure out how to get these apps in sync and make it meaningful, especially for all those people with the blinged out watches who aren't wearing them in the gym or on a hot sweaty run.
Side note: I've been running with the phone 3-4 times a week for the past few weeks and this problem sustains. It never "re-syncs" like some have reported. I don't even get stand credit for the long runs. Ugh!!