The dust collection system will work in either position, though it is not unusual for it work better one way than another since it does change the relative position of some components in the collection area.
Also, keep in mind that there will always be some sawdust build up regardless of how the unit is used since the dust collection system cannot be truly "sealed" without interfering with belt movement. And just like any airflow system, from an engine to a vacuum cleaner, the more resistance there is the less effective it becomes so keeping the collection bag as empty as possible will help. Some other areas that might also lessen effectiveness would be misadjustment of the belt or a loose or damaged impellor.
There are more details in your owner's manual that might also help and you can view the manual online at Manage My Home using your model number and the information in the link below.