As you can see from the ldap config you have two options
-Put all your users that you want synced in one container and use that as a search base (below default)
ldap.synchronization.userSearchBase=ou\=User Accounts,ou=\Alfresco,dc=domain
-Use a custom property on you users that you want synced, and then do a custom query (below default)
synchronization.personQuery=(&(objectclass\=user)(userAccountControl\:1.2.840.113556.1.4.803\:\=512))