Well, first of all you should set the permissions at component level, from the Setup design view, or at file level. To decide what component you should set the permissions on, you have to find out what component the first file that is copied to the folder you want to ACL belongs to. Quite often it's a component named something like "CreateFolder_xxxxxx" or "Folder_xxxxxx". Check the file table to decide the file copy order and what component a file belongs to.
In general it's best to set permissions to the builtin groups, i.e. "BuiltIn\Users", BuiltIn\Administrators", "NT Authority\System", etc, and not to domain groups. If you set permissions to domain groups, the package will only work in that domain (but maybe that's what you want). If you use the builtin groups, you should type the text in to the user column only. Leave the domain column empty.
Use filemon and regmon from sysinternals to track down what files and folders you should set perms on.
One last thing to have in mind when working with permissions; be aware that the ACL’s are replaced, not edited. So don't forget to give perms to the administrators group and system account.