WPMU DEV updates problem

Question 1. I'm new to this, every-time I load a plugin into my muplugins folder I add update-notifications.php for updates but FTP overwrites it everytime. Do I need to rename update-notifications.php for every plugin or just overwrite it everytime????

Question 2. I hit update in WPMU DEV under admin and I get this:

Permission Denied
Not Found / No Access

The page you are looking for either does not exist, or you do not have the permissions to access it.

Thank you