I want to have one user page and multiple project pages hosted by GitHub Pages but available under ONE custom domain (with subdomains for each GitHub Pages
You can either use one CNAME resource record or one A resource record together with GitHub Pages.
So, in conclusion one have to decide:
example.org and www.example.org (replace the existing A record with 204.232.175.78) ...blog.example.org (create a new CNAME record with .github.com ).Now, you have to choose how-to map from one (sub)domain to another:
example.org.example.org and www.example.org to the desired subdomain(s).Also, see GitHub Pages Help for help and my GitHub Pages repository for an example CNAME file.
Edit: GitHub Pages added a detailed page that describes how-to set up a custom domain here.