When you save something or download a file - click " save as " - and direct it to a file on your second HDD.
You create folders and subfolders on your second drive just like your primary HDD - and direct what you want to be stored there - to be stored there. If you go to "computer" from start menu - you can see what's on each drive by clicking on it. If you look up top - you can see new folder - create some and start organizing your files.