Hello Anon,
There is no way to prioritise receive locations in BizTalk, however the engine and FILE adapter is pretty good in delivering multiple files from multiple folders with little performance degradation. The big factor comes when you are attempting to pick-up large files (5Mb+)
There is however a small trick you can implement through the receive location service windows. If, for example, you want to ‘prioritise’ certain locations over others, you could set a service window on the lesser priority locations, shutting them down for a period of time to allow BizTalk to concentrate on picking up files from the higher priority locations.
Hope this helps.
Regards, Nick.