In re how to access the Linux server from a win client, you will probably have to set up Samba to enable communication between the machines. I don't know enough about that to be of much help.
In re the different folders, with different groups, and different permissions, you will have to enable and setup ACL (access control lists), which extend the basic user/group permissions so that different groups (and members of those groups) have different permissions.
is your friend. You will have to do some literature research in order to refine your questions. This is about the best help I can offer.