interesting. Usually it's the opposite - you write it up and your boss signs. Will you hold liability for anything written on the paper? If you are liable, do not sign and convince your boss to turn to someone else. If there' no legal issues involved, then happily sign but never mention anything that's wrong. You boss cares about her face much much more than the content itself. Maybe it's a perfect time to praise what a wonderful job she has done. Believe me, this is the key to keep a long term harmonious work relationship between you and your boss.
You sound a sharp person with talent. But that usually will bring more trouble than luck. Try really hard to say thing you hate to say, as long as it doesn't hurt dignity. On the other hand, she is not supposed to be as technically strong as you are, as she is manager. Her job is to manage you, and she has you to back her up with techniques. IMHO, interpersonal relationship is as important as technical skills.
