In order to change the settings for each plugin, select Capture One 12 -> Preferences… (Edit -> Preferences… on Windows) and choose the Plugins tab. Then select the option to install a plugin from the list on the left and change the desired settings.
Note that the company offering the plugin has made specific settings that are tied to their plugin, so please visit their site for instructions on how to use them. You can disable an installed plugin by selecting it and clicking on the Disable button if you want to turn its functionality off temporarily. Just click on Enable to turn it back on again.
Capture One 12 comes with one plugin from Phase One called Open With Menu. It allows you to exclude certain apps from the Image -> Edit With menu list to keep things nicely organized.