Are there limits to the number of Segments I can create?

Yes, there is a limit of 10 Segments for each application.

Do I have to set up all of my Segments or Funnels up front or can Flurry back-calculate that information for me?

You can add Segments or Funnels to your app at any time and Flurry will back-calculate that information for you. As Funnels are based on Event occurrences, we can only back-calculate to the point in time that that Event was created in your app; the same goes for Segments that are based on Events.

How are funnels calculated? Can a user be included in a funnel more than once?

Funnels are user based, meaning a user can only be counted in a funnel once. If a user completes the funnel multiple times, it will not impact the conversion rate. Additionally, if a user completes the funnel on one occasion but does not on a subsequent occasion, they will be still be counted as a user who has completed the funnel.