I would like my SSH passwords to be remembered automatically when running git pull/push on windows.
I have installed the Microsoft - Git Credential Manager for Windows
The Git Credential Manager is not Working
Environment
There is no magic because the credential helper is for storing https credentials, not ssh passphrase ones for private keys.
Try an ssh agent, as described in "Working with SSH key passphrases".
Note that is ssh is asking you for a password (not a passphrase), that also could be because your ssh public key is not properly registered on the remote site (and it falls back to username/password way of authentication)