CUCM is not a complete replacement for VCS yet but Cisco is incentivising customers to move to CUCM. CUCM doesnt support H323 or name dialing yet, keep in mind even if you have CUCM you will need a Expressway C/E (same code base as VCS C/E but different licenses) for firewall traversal. The expressway C/E does SIP-H323 interworking, so in theory calls to H323 endpoints would work. CUCM doesnt support IP address dialing but there are workarounds in place but these are not user intuitive.
Its difficult to say what the perfect video conference infrastructure since it all depends on what the customer needs to do. If the customer has 3rd party endpoints, VCS would be a better fit.
There is not a single book, you could start at learning the CCNA/CCNP collaboration track and then read through configuration guides and get your hands on some lab equipment.
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