To change your FNIS generation options there is a button on the toolbar of the Mods section named 'Configure FNIS'. If FNIS is installed properly the tool icon will light up. With the required mods installed and deployed, head to the dashboard and click the refresh button on the Starter dashlet. Repeat this process with FNIS Creatures and FNIS Spells (if required). Download the main file with the 'Mod Manager Download' button, then install and enabled in inside Vortex.
FNIS can be installed into Vortex like any other mod.