Install the plugin by downloading the gplugin file and dragging it in to Geneious Prime or use the plugin manager in Geneious (under Tools - Plugins in the menu).
Once installed, run the plugin by selecting your reads and reference sequence then clicking on Align/Assemble - Map to Reference in the toolbar. Minimap2 is available as an option in the Algorithm drop-down menu.
Li, H (2018) Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 34(18), 3094–3100