Hopefully Github's current blast of Issues updates will make it easier for project owners to explain their respective policy on this.
"GitHub issues are for bugs / installation problems / feature requests. For general support from the community, see [StackOverflow](link)"
However, we still get plenty of issues filed that are more appropriate for StackOverflow, so not sure there's anything technical you can do without integrating more closely with StackOverflow :)
Personally, I create an issue if I strongly believe that it is a bug in the project or I want to suggest some improvements (e.g. found some strongly outdated docstrings) and head to SO if I believe that it's me doing something wrong.
But I can easily see how the distinction is very subjective and blurry.
But if I have time I might try to point you in the right direction, in the right forum.