Question: Can you suggest ways of keeping a prayer journal?

Answer: In specific, see the chapter on Journaling in my Spiritual Disciplines for the Christian Life, or the chapters on keeping a journal in Simplify Your Spiritual Life. If you don't have either of those books, the general answer is "Your way is the right way." There is no such thing as "official" journaling. Whatever is edifying and helpful to you (provided it does not contradict the general principles of Scripture) is the way to do it. This also implies that your method may change from time to time.