Both of these have negatives. If you copy everything into the font awesome free folder then you need to remember to copy over the font awesome fonts every time you update.
If you add a line to the startup.html then you need to remember to add the line every time that you update.
Don't make the mistake I did of just over writing the startup.html with a version that you have updated, this will cause you a PITA problem when you get a new feature like Kanban that relies on a new parser being added to the startup.
Also, if you go the route of adding a line to startup.html don't forget to update all the previewXXX.html files - otherwise you won't be able to see your font awesome icons in the config tool