I'll also add that recommended memory requirements haven't changed between 4.5 and 4.6, you would have seen the same warning on installing 4.5. Heap sizes for the existing processes haven't changed in 4.6, but on 2008 R2 the PCoIP secure gateway service will also be installed - when this isn't actively in use though, its memory requirements are very small. For a 50 VM setup the default low-memory installed heap sizes should be fine, are you sure nothing else has changed that would affect the performance of your connection server?
As Linjo said, there are steps in the guide for changing JVM parameters. For reference, HKLM\SOFTWARE\VMware, Inc.\VMware VDM\plugins\wsnm\TomcatService\Params is where you'll find it.