One of the downsides (if it is one for you) of a lightweight processor like WM is getting rid of things like inline comments. I like the comments feature since it doesn't add to the word count, and I can see the comments in the Jumps and address them there.
Not sure of a direct link, but what I do to keep track of where things fall between Repository and the main text is to use similar headings for both sections. So for example:
In my main text:
# 1st Main Point
In Repository:
# 1st Main Point
// Comment
And any text/other research I dump into the repository I can easily reference for the main text.
That being said, if you want thing on-screen for reference, then yeah, my recommendation would be the corkboards.