In Office Communications Server 2007 R2 Microsoft only supports the UC AJAX API in case you add a CWA Server of OCS 2007. The UC AJAX API will not be updated beyond the 2007 release, and programming directly the UC Managed API will be the recommended way to build reach applications. Yet if you want to deploy any existing UC AJAX application, you will need to go through some hoops.

For installing an OCS 2007 CWA server is not trivial in case you start with a fresh install of OCS 2007 R2: it turns out to be you need the AD Schema Prep of OCS 2007 before installing a 2007 CWA Server in an R2 Forest or else the setup will fail. If you want to read the exact steps to take to make this work, please read KB article 969336.

Some people though found there is only one difference between the UC AJAX API in OCS 2007 and API Communicator Web Access in OCS 2007 R2 is using: the URL CommandChannel.aspx became AuthCommandChannel.aspx. And it looks like that everything else is the same. This however does not solve the limitations of the UC AJAX API, such as that it does not support more than 15 concurrent IM end-points per web page. UCMA in any case remains your better choice for reach solutions. Doing it this way isn't supported by Microsoft so you do this at your own risk.