After you've installed Linodef go to Administer → Settings → Input types and enable Linodef for the input type of your choice. Now go to the order page of your input filter (admin/settings/filters/*/order) and move Linodef to the top so it will be run first (i.e. Linodef has the lowest weight). Only that way the other filters can apply their markup to the fields embedded by Linodef. For information how to use the Linodef tags refer to the Input type tips page.