Assuming the paperwhite operates in the same way as the older models I have used, they will let you view PDF files. You copy them across from a PC using a micro USB cable, the kindle shows as an external memory device and you copy PDF's into the books folder the name of which I forget, but I got if off Google!

I'm not sure if you can use folders to organise files, although you might have to try if you have a huge number of files. You can certainly use collections.