Mail Pilot’s Lists are definitely not a replacement for folders, so no worries there. Lists are for when you want to batch process a series of related messages, and track them as incomplete / complete within the group.
Folders on the other hand are treated as a way to organize your completed messages. Moving to a folder is just as easy as moving to a list — just hit your ‘F’ key when 1 or more messages are selected, and you’re off!
Plus, since folders are considered complete, you don’t have to complete your message first — by moving your message to a folder, it’ll automatically be considered complete in the interface.
We’re working on a way to search on part of the folder path — so stay tuned on that. We’re only on the third public beta; lots of ground to cover!