We will be traveling to Florence in September and would like to visit the Ferrari Museum. Is there any advice on doing this from Florence such as trains etc.?
There are also several packages to choose from Ferrari.com. Any suggestions on which ones to choose?

According to Trenitalia, you can take a train from Firenze SM Novella to Modena, and catch a bus from there. You need to coordinate with the (infrequent) bus. Trenitalia gives the details.

Which Ferrari museum? Both?

The Enzo Ferrari Museum and House is within walking distance of the Modena train station. The Ferrari Museum in Maranello is about 25-30 minutes from Modena. There is a transportation service that runs between the museums with a stop at the Modena train station.

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