Geneious Prime itself is multi-threaded, so if you have access to multiple cores you can run several operations at once. However, only the following operations within Geneious are able to use multiple cores in a single analysis:
De novo assemblers
Map to Reference
Custom Blast (Blast+)
None of the multiple/pairwise aligners or tree building algorithms will run on multiple CPUs. These operations cannot be made to use multiple CPUs, as the ability to be parallelised has to be designed into the algorithm from the start.