Something that seems to come up a lot when using git on windows is wanting to use an SSH client to manage keys. When you want to use something like PuTTY its a fairly simple, but somewhat hidden process.
By default, git will look in your C:\Users\<username>\.ssh for an id_rsa key and load that.
To get git to load keys from an SSH client instead, you need to add an environment variable (GIT_SSH) pointing to the directory of the client you are using:
The next time you open a command line tool (cmd/powershell/mingw) git will use the SSH agent instead of loading the id_rsa key.