My helmet, gloves, etc, go into the Givi top box, which is otherwise empty unless I'm carrying the laptop or do some unscheduled shopping - I don't like riding with any weight in it.
Boots go under the desk (spare shoes stay there when not being worn) and jacket goes over my chair back.
If I'm carrying manuals or reference books I use an Oxford Sports tank bag. It has straps to use as a backpack when you take it off the bike, but I don't like riding with a back pack.
Top box lifts off with a turn of the key when it isn't needed.