Note that this is currently a marketing alliance, meaning that you can earn/redeem points on both airlines, and their websites link together, but there are no code-shares.
Frontier CEO Sean Menke has gone on record stating that he things the LCCs should form closer alliances, and apparently it has been technical issues (likely software development) which has stood in the way of Frontier/Airtran codeshares, but that's what they have as a goal in the future.