Is there a way to have a second desktop which you can put individual folders and files on it, so that the first desktop is clear without any files?
Yes you can. Mac refers to the extra desktops as spaces. You can create up to 8 extra spaces I think and you can control them from Mission Control. The control key plus a digit will make that particular space active.
if you go to Mission Control (probably in your doc) a window opens showing all the spaces across the top. There is also a plus sign. Clicking the plus sign creates a new space. I find spaces very convenient. I have a space set up for one app and another space for a different app.