Step 1: Make Your Folder
Step 2: Create Sub-Folders
After you make your folders, organize your PDF's according to the Primary Folder they would be (ie, arduino w/ tech, wood stove w/ workshop etc.)
Then dive into your Sub-Folders and further segregate the PDF's by the Sub-topic they stand in ( ie, tech/usb/deaddrops, food/drinks/bahama mama, etc.)
Personally i leave the e-books out of the sub-folders. BUT if you feel inclined to do so, you can create a specific E-Book/guide sub folder.
The following images is what your folder setup should look like.