Can I enable FileVault and then partition my hard drive later? I just bought a 2014 MacBook Pro with a 512GB SSD. I updated to El Capitan today and when it booted up for the first time, it asked me if I wanted to enable FileVault. I chose not to because I wasn't sure if I should enable it before I install Windows via BootCamp (and possibly a Linux disto too).

So, should I enable FileVault now and then partition my drive later for the other OS(es), or should I wait until I partition the drive? Thanks!
Yes, you will be able to partition later. When you partition, both partitions will be encrypted with FileVault.

Alternatively, you could just set it to encrypt your El Capitan partition, it won't make a difference.