I have about 200 torrents in the queue and have it set to maximum seeds = 5.

However, the 5 torrents it is seeding is not uploading anything. If I switch to manual and select all my torrents then about 6 -12 start seeding at a slow speed.

Is there a way to set up the queue manager to run down the queue until it starts to upload something?

In settings -> Queue Manager there is a checkbox titled "decrease priority of torrents which are stalled for too long", you should give that a try."