We've always requested/reserved an automatic- we book with autoeurope and if the location does not offer automatic it will indicate that.
With autoeurope you do pay in advance but it is completely refundable and they are quick about it (I just had to cancel a rental with them and refund showed up next day).
If you pick up in Florence- there are several locations-- we used the Sansovino Hertz location first time. We will use the Borgo Ognissanti the next time (near train station).
Search this forum for "car rental Florence" and look for responses from Roberto- he is a Florence native who always gives very clear instructions for where to pick up and how to get out of there avoiding ZTLs.
Be sure to read up on ZTLs, speed cameras, parking/driving in Tuscany and all drivers MUST have an IDP- International Driving Permit- you can get this from your local AAA office about $15-20.
Some advice from our experience- we had an automatic reserved and when we got to the location (Sansovino) there was only 1 automatic left on lot, it was a van and a large one at that- we panicked a bit but took it anyway and it all worked out well. I had done a lot of research on parking at our hotels and parking garages etc so we did not have any issues with that big van.
My advice is to get to the pick up as early as you can to avoid the possibility of all automatics being gone. And no matter where you pick up get clear directions from the agent on how to exit without getting tangled up in ZTLs.