GitHub allows you to attach a deploy key to any of your repositories. However, each repo must have its own unique key. If you’re deploying multiple GitHub repos on a single machine, that means you’ll need to set up multiple ssh keys for that machine. The easiest way to achieve this is to leverage ssh’s host config. If you have mygithubuser/repo1 and mygithubuser/repo2 that you want to deploy on a single machine, first create an rsa key pair for each repo:
ssh-keygen -t rsa -f ~/.ssh/repo1_rsa -C "repo1 deploy"
ssh-keygen -t rsa -f ~/.ssh/repo2_rsa -C "repo2 deploy"
Cat the public keys and copy+paste them into each repo’s respective GitHub deploy key: