If the checks are checked but gray it means that the permissions have been set at a higher level. If you want to override the global permissions (ie the permissions set higher up) then uncheck the box that says "allow inheritable permissions from parent to propagate to this object", then click the remove button when it pops up--this will remove any usernames that were in the upper box, since they were being inherited from above. You can now go back and add whatever users you want and give specific permissions to each user.
Now if you want these new permissions to propagate to all subfolders under the folder you are in, click advanced and check the box that says "Reset permissions on all child objects and enable propagation of inheritable permissions" NT 4 had a much simpler way of saying this, but this just sends whatever permissions you just set in the upper folder down to any subfolders and files that may already exist or will be created.
I hope this helps a little, I find that win2k server editions are kick ass OS's and are very powerful when it comes to permissions. If you dont mind me asking however, what are you using an os as powerful as Win2k AS for?