I'm making the move back to ownership (must be the beer talking), and was wondering how the flex cost works if I bought a team now (midseason) rather than waiting til the end of the season? The last time I owned I did it the easy way and bought during the off season. Is it prorated or what?

It's indeed prorated. Traditionally (when you buy in the offseason) you get 2 seasons for your 1000 flexies. When you buy during the season you essentially pay for the rest of the current season and then the full next one.