Hello, & Welcome to Tom's Hardware!
If you want to use your D drive for storage, there are several choices.
1. Simpliest is to just create a file structure on D, and save to those folders
2. Instead of having a "D drive", you could instead create a separate empty folder in your Documents, say Addt Storage, then "mount the drive" (Disk Managment) to this folder. Then to save files, you would choose "My Documents", Addt Storage. They would be saved on the secondary HDD.
3. You could set up a file structure on the D drive, like "Addt Documents", "Addt Photos" etc. Then click on the folder you just set up, on the toolbar choose "include in a library" and connect it to the library on your C drive of your choice. That way in your regular file structure, the "Addt Documents" will apprear, but it's actually on the D drive.
Here is the Microsoft explanation of how that's done:
http://windows.microsoft.com/en-US/windows7/Include-folders-in-a-library