How do I add sections that are only seen and used by the end user?

For example i have employee evals and would like to place my own comments on the submission and resend back to the employee fro review. 

You could set up an admin section of your form or a set of hidden fields for comments.  This thread here describes how to setup a full approval workflow if you'd like:

http://www.jotform.com/answers/401633

However, if you only need the section for reviewer comments, you would only need to include the admin section and have the edit link sent to all the reviewers.