If you have already encrypted files, are they still vulnerable to being encrypted a second time by a program like Cryptolocker, or would this protect them? 
Yes they are still vulnerable. Encryption just transforms a sequence of bits into another sequence of bits (and assuming the encryption is good it will be computationally infeasible to reverse this process without knowledge of some secret). There's no reason why encryption can't be performed again on an already encrypted sequence of bits.

It's possible certain ransomware implementations might look for specific files that are likely to be of high value, and encrypting these files might make them more difficult to recognise. However, I would not depend on this as my primary control against the threat of ransomware.
