Hi Glen,
Method is designed to be used as an add on to QuickBooks, and always connected. Although it is possible to use Method on its own, you won't be able to take full advantage of the platform so this isn't recommended. It is probably due to to the disconnection between QuickBooks and Method that you are getting the customer cannot be found issue.
However I don't recommend reconnecting Method to QuickBooks right away. Since you deleted the contacts in Method, the sync will try to delete the contacts in QuickBooks as well - probably not what you want. If you would like, I can reset your Method account so that you can start fresh again.
If you would like to set permissions for what your employees can see and do in Method, there are many ways of doing this. For example you could create a role for all your junior salespeople, and hide certain data or screens from this role. For more information on roles in Method, please see this link: https://www.youtube.com/watch?v=_AnvoII55U0&feature=youtu.be&hd=1.
Hope this helps!
-Russell