No option to boot into windows now I've installed El Capitan
This guide will help you fix the problem. I had a similar issue on mine. Make sure to back up your entire disk (both partitions) before making any changes though. No joke. Believe me, it's important. Buy an external drive if you don't have any place to back it up. (When people used to warn me to take backups, I didn't listen, and I once lost 6 months of data because of that.)

Please also see this answer to find out how to turn off SIP protection in El Capitan. Without turning this off it won't be possible to repair the Master Boot Record.