A list of tools offered by the CLC Genomics Workbench and the CLC Genomics Server that benefit from the availability of multiple cores is at:
http://resources.qiagenbioinformatics.com/manuals/clcgenomicsserver/current/admin/index.php?manual=Use_multi_core_computers.html
While these tools benefit from computers with multiple cores, it does not mean all cores available are used the whole time.
For information relating to using large system (>64 cores), please refer to https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Limitations_on_maximum_number_cores.html