Thank you for installing the Geneious PhyML plugin.
The PhyML tree builder is available when you click "Tree" in the toolbar at the top of Geneious.

If you use PHYML, please cite:
"New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0."
Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O.
Systematic Biology. 2010 59(3):307–321.
This is a detailed description of the algorithm.