I use marked messages as a task list. They represent things I need to take care of. As such I always keep the number of marked messages low and I defiantly prefer to have them in my face as much as possible. Based on the feedback so far I think Anaris' suggestion of letting the player choose which route to take would be ideal. I know I would dislike having to go digging for my marked messages just as much as others dislike having them in their face all the time.
