Let's say you want to give a machine access to one of your repos but not all of them. This is a reasonable thing to want, and so GitHub offers deploy keys. But what if you want to give it access to two repos?

The natural thing to try would be to add the same public key to your second repo, but GitHub rejects this:

Error: Key is already in use

I think this error is because they don't want you to get into a situation where multiple machines are using the same key. If that happened and you needed to revoke one machine's access, you'd be stuck. In this case, however, we only have one machine and we're trying to use the same key for two repos. I don't see any issues with that setup, and while maybe I'm not being imaginative enough I think GitHub should probably be checking for duplicate deploy keys on a per-repo basis instead of globally?

Still, what can we do with GitHub as it is? Generate more keys and use aliases!

I'm going to walk through this assuming you're starting from scratch trying to check out both github.com/you/repo1 and github.com/you/repo2. If you already have repo1 working and don't mind having the two repos configured differently, just follow the repo2 steps.

First, generate a ssh key for each repo:

$ ssh-keygen -t ed25519 -C "machineName-repo1"
Enter file in which to save the key: /home/you/.ssh/id_ed25519.repo1
...

$ ssh-keygen -t ed25519 -C "machineName-repo2"
Enter file in which to save the key: /home/you/.ssh/id_ed25519.repo2
...

Then visit github.com/you/repo1/settings/keys and github.com/you/repo1/settings/keys and paste the contents of ~/.ssh/id_ed25519.repo1 and ~/.ssh/id_ed25519.repo2 respectively.

At this point you've created the keys and told GitHub to respect them, but you haven't told ssh on your machine when to use which key. You do that in ~/.ssh/config:

Host github-repo1
     HostName github.com
     User git
     IdentityFile ~/.ssh/id_ed25519.repo1
     IdentitiesOnly yes

Host github-repo2
     HostName github.com
     User git
     IdentityFile ~/.ssh/id_ed25519.repo1
     IdentitiesOnly yes

Anyway, now you can check out your repos:

$ git clone github-repo1:you/repo1.git
$ git clone github-repo2:you/repo2.git

The reason this works is that git, like anything else that uses ssh, doesn't actually interpret the host name or set up the connection. It just asks ssh "please connect me to github-repo1" and ssh will use aliases as part of figuring out how to do that. This also means that almost any time you might have used GIT_SSH_COMMAND, or otherwise passed arguments to ssh, an alias is a better choice.

If you'd already checked out your repo, however, instead of checking it out again you just change where origin points:

$ cd repo1
$ git remote set-url origin github-repo1:you/repo1.git

And the same for repo2.