I am not sure I understand what you're asking exactly, BUT. . . .to download books via your PC you go to the usual Amazon book page and just use the drop down box to indicate 'transfer via computer'. When you do that it downloads to your computer. THEN you connect your kindle via USB. . . .you should be able to see the 'documents' and other folders on the Kindle and can drag and drop from where it's stored on the computer to the Kindle.
I expect you know all that.

From your post above, it sounds like maybe your computer is not recognizing the Kindle as a drive and seeing the sub-folders. I think this is an issue with your system, not the Kindle. All I can suggest for that is to do a restart of the computer, maybe with the Kindle connected.
I can say for certain that I tried to connect once with a cord that should have worked just fine but didn't -- Kindle indicated charging but computer didn't recognize it as anything. When I used the cord that came with the Kindle I had no problem and was able to transfer files.
Others may have some other insights. . . . .