Ubuntu does not use drive letters; it sees all of its available space as one large tree. It lists your Windows drive (which is called "C:" in Windows) as one of its "Devices", as you mention, but that is just a matter of convenience: in Ubuntu terms that is probably a folder called /media/long-complicated-drive-name/.
The fact that you can see more files in Ubuntu than in Windows is more like a Windows trick: under Ubuntu you will see all files and directories, whereas Windows hides these from you.
The boot, etc, dev, root, run etc. are system folders where you shouldn't store anything, and in most cases, the system won't even let you. Feel free to organize your own files in the /home/username folder. That one is comparable with the folder called "username" under Windows. Ubuntu does not care how and where you store things in /home/username, except for personal settings which are typically in folders starting with a ".".

From the Windows perspective, whether your Ubuntu system is stored in D: or J:, or somewhere else, is impossible to tell without more information.