I stopped taking my birth control pill (Ortho Tri-cyclen lo) almost two and a half weeks ago after my last period (beginning 9/29). I am now having my second period of the month (beginning 10/13). Should I treat this as if it is a regular period? How will I know when I am going to ovulate again?

It could be anovulatory bleeding. I highly recommend the books Taking Charge of Your Fertility or The Art of Natural Family Planning if you are interested in tracking your cycles. It will enable you to identify ovulation and predict your period. And it will also let you know if you are having anovulatory cycles. The only way to know for sure is to chart your temps and cervical fluid.