Passwords are not synched, even if you synchronize with LDAP, Alfresco will still authenticate by looking up the users in the LDAP directory. However, this cannot be done with CIFS connections, because of differences in the password hashing, so you need to have Alfrescos internal Ntlm authentication enabled if CIFS access is going to work. Of course this means that you have to keep your passwords synched somehow, between your Alfresco server and your directory server, if you wan't your users to be able to use the same password everywhere.
One solution to that might be to set up a common backend, such as a Samba Domain Controller.