Yes, with CiraSync Enterprise Edition, you can create multiple contact lists. For each contact list, you can define the source where CiraSync will pull the contacts from, and the target users who will receive the synced contacts in their mailbox and smartphones. This is done through the Contact Collections functionality.
Use the Contact Collections functionality to define a subset of the GAL, so it can be used either as a source or a target inside the Contact List. If you add the GAL (All Mailboxes or All Contacts) into the collection, you will be able to expand and exclude unwanted members. Once the collection is cleaned up, you can use this collection as a source or target in your contact list.
Learn how to create a Contact Collection with Creating CiraSync Contact Collections.