You can now upload email addresses (into Matchday and Whole Game System) for your players via. The FA Matchday App.
If you go to the Fixtures tab > Matches > Click on Fixture > Squad > Click "Invite Players" button
You will then be able to input email addresses for each of your players.
Please be aware this will not automatically send an invite to the players and that players must login by using their email address you have inputted and their FA Account Password - this can be set here: https://www.thefa.com/account/RequestPasswordReset