So far I’ve gotten this partially solved.
When you create your new repository on sourcetree you need to uncheck the box that says “create repository on account”. If you do this, source tree will see that your folder doesn’t have a .git file in it and ask if you’d like to create it. Choose yes and it will be properly added to your sourcetree. However, at this point it isn’t synced with online yet. I’m trying to figure out how to get it to sync with github, but this will at least allow you to create it in sourcetree properly at this point.
See this url, last response, this will add github: https://community.atlassian.com/t5/Sourcetree-questions/How-to-put-a-new-project-to-github-with-SourceTree/qaq-p/241446