Well episode 13 was set in the 年 2019 so unless Dollhouse runs for another ten seasons, I don't think they will continue it! When season 2 starts, it will probably continue on from the end of episode 12 with Alpha leaving and everything. Plus, episode 13 never aired so unless they changed their mind and aired it, I don't think they could go back to that storyline without some form of catch up. So basically they will carry on from episode 12.
as that episode was just an addition to joss's script, i think seeason2 will continue from episode 12, however i definitely thinik they will slowly exlain some of the things from the bonus episode, throughout the season. CANT WAIT!