You don't need to get Downloader to store them in a single folder. In Metastock you can create a folder in 'favourites' for the whole market, and add all the stocks to that favourites folder. They are still stored in the seperate folders on the hard drive (I group them by industury group rather than A, B, C, etc), but you can access them all through the single favourites folder within Metastock.
The way to do this is to do an 'exploration', add the contents of every folder to the list to scan, then click to save that list to your favourites.