Apple Watch and Runkeeper

Here is the scenario:

Typically, when running outdoors, the Apple Watch and Runkeeper don't double count data because it is happening at the same time and the watch knows that.

However -

I sometimes run on the treadmill and indicate on my Apple Watch that I am running indoors.

After my run, I manually enter the treadmill data into my Runkeeper where I track my overall running goals.

Because run keeper is paired with my watch, and I enter the data manually after my run (in other words the data input isn't happening at the same time as it would be when I run outdoors), is the watch double counting Runkeeper?

How do I stop this from happening?