As you authenticate with your ssh-keys, you should use a different ssh-key for each account.
You then need to configure the ssh-key used for pushing changes, which then again determines the account to authenticate against github.
You can do this, by setting a different core.sshCommand for each local repository.
The following example assumes repo1 is using ~/.ssh/key1 and repo2 is using ~/.ssh/key2.
In repo1, you set core.sshCommand to use ~/.ssh/key1 like this.
git config --local core.sshCommand "ssh -i ~/.ssh/key1"
In repo2, you set core.sshCommand to use ~/.ssh/key2 like this.
git config --local core.sshCommand "ssh -i ~/.ssh/key2"
To configure core.sshCommand while cloning a repository, use the following command
git clone -c core.sshCommand="ssh -i ~/.ssh/key1" git@github.com:repo1/repo1.git
Note that this must be done for every local copy of the github-Repository, and also may not working if not using a Unix operating system or the git bash for windows.
Also see this answer