Install the plugin by downloading the gplugin file and dragging it in to Geneious or use the plugin manager in Geneious (under Tools - Plugins in the menu).
Once installed, run the plugin by selecting your reads and choosing Tools - Merge Paired Reads using FLASH 1.2.9 from the menu.
FLASH: Fast length adjustment of short reads to improve genome assemblies. T. Magoc and S. Salzberg. Bioinformatics 27:21 (2011), 2957-63.