You can find more details about RadUpload tool on Rad Upload for ASP.NET Ajax
page. There you'll see some sample code and different implementation scenarios, that I believe fit yours. Setting the TargetFolder property for the RadUpload tool is very easy and allows you to point each upload tool on each page to different folder in your file structure.
However, the Download List gets its source from your Image, Documents etc Libraries. If you want to set this up, what I'd suggest is to take a look at the JobsIntermediate module in the Visual Studio Sample solution, that came with your Sitefinity installation. There you can see the way uploading applications to Libraries is handled - follow these examples to set your upload tools to upload to different library for each page, and then set this library as a source to the Download List.
I hope this information helps. Please let me know if I can assist you any further with this service request. Thank you in advance.
the Telerik team