There really is not a "what if this happens" type of doc.
It's basically, you learn the proper way to assign rights and don't deviate from it.
The hard and fast rules are:
Admins (domain and local) and System are the only ones who are granted full control over any files (no matter what!)
Users (any one other then the admin group) are granted nothing higher then change. Never Full.
Domain admins/Local admins are the only group that can take ownership of files.
Never control access thru share permissions, share permissions should always be everyone=full.
Never give NTFS permissions everyone=full.
An example would be a users home directory:
Admins = Full
System = Full
User = Change
Another tip- Only assign groups to folders never individual users. With the exception of the users home folder.
Why? 2 reasons. 1, it makes it easier to add more people to the resource by just adding them to the resources group. And 2, If I the hacker, enumerated the rights on a resource and found usernames, I then have a valid username to use/try out.
Also, I always prefer to use the Local Administrators group when doing permissions rather then Domain Admins. As long as a machine is joined to the domain, then thedomain admin group is automatically in the local admin group.
With these basic concepts you should be able to administer your permissions.