Can you post a picture? I do not see duplicate workout data in workout, activity, or health on the phone or watch when I run with RunKeeper and Workout. In fact, I can't find anything from RunKeeper at all.
ok... nothing can write to the workout or activity apps bar the watch. so there will never be duplicate data of that - well not until os2 and i'm pretty sure they'll have ways to deal with this eventuality and prevent duplication.
in health, runkeeper writes different data for different activities. for all, it will write your active calories. beyond that, it depends. for running and cycling, it'll log a workout and also the distance ran or cycled. for others, i don't think it writes anything but the active calories.
in the health app under workouts, i often see this if i've cycled on the machine and used both "workout" on the watch and runkeeper on my phone:
but the health app graph will only show one of them - or if they're mismatched by a minute for example, it'll show the start time of the earlier one through the end of the later one as "workout time" on the graph. If i did an hour of workout and logged it in 2, 3 or 4 apps at the same time and they all wrote to health, then the graph would only show me as working out for one hour. it knows how to deal with multiple entries.
under active calories, I have my apple watch as the top source on the list. I have lots of other apps which populate the data but health ignores them and at the end of the day the total given is basically just the same as my watch, no matter what other apps say
(picture to follow when it loads the data in active calories)
under the sources tab at the bottom, do you have runkeeper enabled to write data in healthkit??
Strava and Workout can run simultaneously, just make sure you disable health kit upload for Strava(or Workout depending on which data you want added) or you'll get double data appearing.
I use Workout app to upload my calorie burns/workouts to healthkit
MyFitnesspal takes calorie burn data and workouts from heathkit
I log Cyclementer when I'm on my bike and upload that data to Strava separately.
Neither of these apps are allowed to use healthkit and operate within their own ecosystem to prevent double data.
When the Applewatch allows 3rd party apps to log HRM i'll probably stop using Workout and just use Cyclemeter to log workouts in Healthkit.
i was going to say there's no need to do this, but then I saw how you use myfitnesspal. the problem isn't with health itself, but how myfitnesspal reads it. it isn't equipped to do it properly - if i log a workout in two apps it will indeed show up twice in myfitnesspal. this is one of the reasons why i stopped using it and moved back to a different app to log food intake.
but unless OP is set on using myfitnesspal in this way (if it is used without reading healthkit data, its not a problem anyway) then there's no need to copy your setup. the health app can handle double, triple, quadruple data quite well and display it on the graph properly. you can log a workout in health and runkeeper and - if you view it in health - the data shown back will be as it should (according to the priorities you put on each app, under the sources list). [the only exception to this is runkeeper, if an activity is logged manually it will often duplicate it's own data and the health app can't handle that. it needs one of the entries to be deleted manually in the health app, which is annoying. but doesn't happen under the stopwatch mode)