The other day I was looking into hosting websites on GitHub Pages, and I found myself wondering if it’s possible to host multiple custom domains for a single GitHub account. I came to the conclusion that it isn’t possible. You can use one custom domain per account, and that custom domain can effect different types of repositories within your account. For instance, if I used megancoyle.com for my custom domain, it would be the new URL used to access my GitHub site page that was previously accessed via megancoyle.github.io. Then project pages would no longer have the URL megancoyle.github.io/hangman, but would use megancoyle.com/hangman instead.
So if you want to keep your other repos more separate from your personal page, you may want to rethink how you use a custom domain. Or you’ll possibly want to think about how you’d like to brand your different repositories.
Here are a couple of articles that can help you with linking your domains to GitHub Pages: