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 assembly
Flye (Geneious Prime 2020 onwards)
Map to Reference
Minimap2 (Geneious Prime 2020 onwards)
Clustal Omega (Geneious Prime 2020 onwards)
Custom Blast (Blast+)
None of the 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.