<p>I'm developing a client/server app that will communicate via rest. Some custom request data will be stored in the header of the request. Both the server sending the request and the receiving server have an SSL certificate - will the headers be encrypted, or just the content?</p>

SSL encrypts the entire communications path from the client to the server and back, so yes - the headers will be encrypted.
By the way, if you develop networked applications and care about data security, the least you should do is read a book like Practical Cryptography, by Niels Ferguson and Bruce Schneier, and probably further reading that's more focused on web application security would be a good idea. If I may make an observation - and please, I don't mean that as a personal criticism - your question indicates a fundamental lack of understanding of very basic web security technologies, and that's never a good sign.
Also, it's never a bad idea to confirm that data which is assumed to be encrypted is indeed encrypted. You can use a network analyzer to monitor traffic on the wire and watch out for anything sensitive being sent in the clear. I've used Wireshark to do this before - the results can be surprising, sometimes.