Ubuntu Servers :: Samba Shares Using Active Directory Permissions?

I am the IT Manager at a research facility. We have a fairly unique network configuration in order to support all of the different projects we have going on. We have Red Hat, Ubuntu, Windows XP/Vista/7, Windows Servers 2003, Ubuntu servers, Red Hat servers, and even a few Netgear ReadyNAS and Buffalo Terastations. Over the last few years, I have been migrating all of my users and accounts to a single ACL list, which I chose to be a Windows AD 2003 server. 95% of my users work on Windows platforms and just use ssh tunnels to develop on our linux boxes.

However, i ran in to a problem with our Linux boxes not being able to symbolic link on my Windows 2003 file shares. Of course, this is a problem with Windows not supporting symbolic links. I know 2008 does support this feature, but given the economy and the budget restraints, we cannot afford to purchase the updates we would need, so now I am moving all of my shares to a Ubuntu 10.04 server using Samba. I have joined the server to my AD domain successfully, i can login using my AD credentials, and even assign ownership and group permissions using AD users/groups.

Here is my question.

I would like to keep the AD permission schemes intact. I have several shares that contain folders that have individual permission settings. For example, I have a /shared directory that contains about 50 different folders. Some of these folders I allow my users to write data to, some just read, and others I deny access to complete groups and just allow key groups to access (for example, personnel data should only be accessed by the Administrative staff).

Is there a way to make this work?

I can assign uid and gid manually per folder in Samba, but i would like to have the possibility to add multiple users and groups with permissions to folders, which I do not believe can be done with the standard chown commands. Currently, I can see the folder permissions from my Windows box, but when I try to edit the permission settings, it defaults back to full access. So my AD permissions are not being saved.