You need to set up Group Policy objects for the OUs that load the different logon scripts. One GPO is all you need for each different logon script.
1. To create a GPO you need to right-click a the domain icon or OU in the tree (Active Directory Users and Computers) and choose Properties. The Group Policy tab is used to create new GPO (Hit New). Highlight the new policy and then hit the "Edit" button. You'll have to look around in there but eventually you will come across the Logon and Logoff scripts under the "User Configuration" settings. Add the desired script to this interface.
2. Once you have created a GPO for EACH different Logon script you need to go back to the Group Policy tab. This time, highlight the Group Policy object and then hit the "Properties" button. You should see a "Security" tab that looks like NTFS permissions. First, remove the "Authenticated Users" group from the list of groups. Add the group you want the policy to apply to and look at the bottom box. The last permission in the list is "Apply Policy". Check this box and the policy will be applied only to members of that group.
* Note that the GPO is going to apply to the Site, Domain, or OU that it was created on. With the number of OUs in your domain I would suggest creating each GPO on the domain. This way the script will run for the user based on group membership, regardless of where in Active Directory it is created.
If you put a different set of mapped drives in each script, they will end up with different mapped drives based on the groups they are a member of.
