Now that we’ve purchased online our Firenze Cards, what’s the best way to go about booking specific museum times?
Reference the FAQ page of the Firenzecard website for making timed-entry reservations for the museums (Uffizi, Accademia and duomo cupola) which require them. The one you can't make a reservation for prior to arriving in Florence is the dome (cupola) of the duomo.
http://www.firenzecard.it/index.php?option=com_content&view=article&id=20&Itemid=119&lang=en
Scroll down to "Do I need to make reservations for the Uffizi and Accademia Gallery with Firenzecard?" and "How can I book the Cupola climb with Firenzecard?"
You don't need timed-entry reservations to enter any of the other museums the card covers: just show up. I will recommend reading the entire FAQ page carefully for understanding how the card works.