The rules that you want to apply to the organisation of your garden shed are the same as those used for any indoor space. Do not think of the shed as something more confusing to get into working order than say your kitchen or bathroom. All of the areas you live or work in need to fully function, so why should they be any different from one another.
To get stuff into order, the best way to figure out what you are working with is to take everything out of it. Yes, we know you are groaning over this, but it really works. Put the items from within the shed into allocated sections. Identify each with a title such as regularly used, sometimes used, rarely used, should be eliminated, and need repair. Then place the items most often used in very easily accessible places, and follow with the others accordingly. Create a plan of action on how to get rid of those items no longer needed, and when and where you will get the remaining bunch of things that need repair, well repaired.