Time Machine and FileVault

After reading a (reasonably scary) article about Mac security, I've decided that I think I'm going to start using FileVault to encrypt my HD (just for security, etc). However, I use Time Machine, but don't want my backups to be encrypted, as there's really no need. Will it automatically back up them up encrypted once I enable FileVault, and if so, how can I stop the backups from being encrypted? Also, will my Windows partition be encrypted as well? And if yes, will it affect Windows at all?

Thanks!