Can i make a run recorded under the 'course activity' count towards my weekly run total on the watch (945)

Don't know what you mean with a "course activity", but when doing a run activity you can choose to follow a course. After having selected Run, press Up for options and find the courses that you have saved and transferred to the watch of type Running.

You can edit the Activity and then change the activity type using Phone App or Garmin Conect Web.

Thanks that is the solution I was looking for. My mistake saying 'courses' activity. It was the 'track me' activity I used and followed a course in that via the options. Is the 'track me' activity for creating a course/route in 'reality' rather than creating the course on the the computer/app first? 

I've never used the Track Me feature, but even so - when I tested just now - you actually need to start navigation or something else, don't you?

I found this in the forum as well.

It’s basically just a simple sport mode that includes the ‘map’ view (so breadcrumb on non-5X units, or with maps on 5X units).

I suspect Garmin made it to simply keep things simple to explain to someone in a support/store/etc scenario as to what mode to use to get a map while doing an activity.

https://forums.garmin.com/outdoor-recreation/outdoor-recreation/f/fenix-5-series/126798/what-is-track-me/704896#704896

The Track Me activity type is something you can use when you just want a track logged during whatever you do and don't want to use run, walk, hike, bike or something else to not mess up the statistics for those activity types. Use Run and select the course and everything will be as you wish.