I login in with Administrator on Vista with UAC turned on, is it OK for me to create, modifty or delete file in ProgramData folder. My test result is YES, but I found my AP can access the folder which name is "MicroSoft", is there any starndard document to know the ProgramData folder's right under Vista?
It should be fine, yes. The Program Data folder is there for programs for that purpose.
In terms of permission, you should be able to check or modify file permissions using .NET. See the System.IO.DirectoryInfo class as a reference, and see System.Management and System.Management.Instrumentation namespaces for getting user information.