Create Custom Domains for Multiple Github Pages Repos

Nothing special, just create two different CNAME records, and both points to [username].github.io.

For example, the first github pages project is [username].github.com/project-a, and it's published at [username].github.io.(The first github pages site will be published at root). You can create a custom domain CNAME record like project-a and point to [username].github.io. Then you can create the second github pages project at [username].github.com/project-b, and it will be published to [username].github.io/project-b. The trick here is that you only need to create another CNAME record like project-b and still point to [username].github.io. Now you have two github pages sites project-a.[you-domain].com and project-b.[your-domain].com.