I've been trying to get git working on my laptop using both my github.com account and my github enterprise account. I've been following this guide and this one to figure out how to edit the SSH config file and get authenticated. I also looked at this SO question which is pretty similar, and did the ssh-add mentioned on there (for both keys).
So in total, I created separate public keys in the different folders (github and github_enterprise) and added them on both accounts online. I then edited the SSH config file to include the different sites, usernames, and keys, then did an ssh-add (ie: ssh-add ~/.ssh/github.com/id_rsa and ~/.ssh/github_enterprise/id_rsa). I tried to ssh (by doing ssh github.com or ssh github_enterprise), but it times out and I have to do control X-C.
This is my SSH config file:
Host github.com
HostName github.com
Port 4096
IdentityFile /home/my_username/.ssh/github/id_rsa
User my_github.com_username
Host github_enterprise
HostName github_enterprise
Port 4096
IdentityFile /home/my_username/.ssh/github_enterprise/id_rsa
User my_github_enterprise_username