After much reading of documentation and GitHub issues I have realised the following:
Personal GitHub account/GitHub pages do not have access to a gh-pages branch nor a /docs folder in master.
User accounts only have access to a master branch, meaning index.html will be served from there. This puts the brakes on my plans to incorporate a Circle CI build into this workflow for the moment and leaves with a rather messy private repo which is not in sync with my true repo. I will need to look into how to resolve this since at present, my true master branch contains the Gatsby source files along with the markdown files that are the source of these blog posts.
The problem is that the GitHub repo is now actually the /public folder, which is not really what I want to keep in source control since it muddies up the repo. Use of a /docs folder would have resolved this for me, but alas, my account does not allow for it.
I took a very brief look at the options when adding a new repo, as well as for signing up a 'Project' on GitHub, but I am not quite sure how or where this is defined. It seems to me that I will need to look into alternatives for hosting my development blog since GitHub Pages does not quite suit my needs when it comes to managing and serving the code.
Another topic I took a look into was moving all my .md files into their own folder within my 'src' folder. This only half-worked, since it seems to mess up the routing of my links as well as the build at times. I will need to look into this further because it bugs me that I have .js files mixed in amongst a whole lot of .md files. Anyway, its a nice-to-have so I will get to it at some point.