Generally speaking, yes you do. The process is very meticulous as only you know what is important to you and what its emotional value might be. Just like only you know if the organizing systems that I might suggest will actually work in your home/life. Being fully involved in the process is extremely empowering and the energy that is created will help you to maintain systems for a better organized life. Saying all that, once I understand your specific goals and personal style, there might be parts of the project that I can work on alone, while you are working in another room or running errands (or in some cases while you are at work). This of course must be discussed and agreed upon early in the process.
Do I need to be present for the whole time while you are there organizing?