I heard once that flat ironing damage can "travel" up to your new growth...e.g. split ends will keep traveling up if you don't cut them. So I'd advise you not to flat iron your ends excessively. Also, I think transitioning is a good time to start practicing healthy hair habits for ALL of your hair -- so minimal heat is optimal. Good luck!
Last relaxer: September 2011
Follow my progress on my transition blog: http://naturallycurlyjourney.blogspot.com/