As a general rule of thumb, I've submitted my FAFSA to any school at which I interviewed and I'm still considering, regardless of whether I've been accepted or waitlisted there (unless rejected by that school post-interview.) Most schools tell you to submit a FAFSA to them even if you haven't been accepted yet, or even if you've only had an interview and haven't heard back.
Also, each school seems to have a good financial aid website that specifies what you need to do by when. Generally, submitting your FAFSA is enough for now, but some schools have their own forms due soon (like Loyola's FAA due March 1 online.)
Finally, the FAFSA website has pretty good help info for how to complete the FAFSA.