You will have to do that manually. GCM doesn't care about user accounts. It only cares about the device itself. In your case I would register device with GCM once and then reuse the same registration ID for all your users, meaning that when sending GCM notification you will have to include some identification data to know for which user you are sending that particular notification.
So in a nutshell: register your device with GCM once and then send registration ID you receive + all custom user accounts IDs to your application server. When sending notification, add user ID into notification message and then use it to determine to which custom account user it is intended.