Often when using your computer, your desktop will be covered by the various applications you use. In many cases, people will almost never see enough of their desktops to make it of any relevant use; however, others regularly close, hide, minimize, quit programs and organize files on their desktop for the convenience it offers.
If you are one of these people, then OS X offers several options for organizing files on your desktop. These can be invoked by clicking on your desktop, and then choosing an option from the View menu to sort Desktop items. This is also available by right-clicking the desktop and choosing a sorting option from the contextual menu.
While the sorting options Apple provides can organize files by type, name, creation and modification dates, among others, if you wish to manually sort the items then you can by selecting "None." You can also select "Snap to Grid" which keeps items on your desktop from overlapping.
This option allows you to place items anywhere on the Desktop without them snapping back to a predetermined location. If you choose to use your desktop in this manner, then there is a way to provide an organizational scheme for your desktop items by creating a custom desktop image that will section off areas for specific file types, or for specific aspects of your workflow.
To make such an image, you can use some of Apple's built-in features. First, create a screenshot of your desktop by pressing Shift-Command-3. This will place the image as a PNG file on your desktop, which will open in Preview by default. When opened, press Command-A to select the entire image and then delete to clear it. Now you can use Preview's annotation tools to add lines, circles, squares, and other shapes to section off areas of the desktop image for your various uses.
For example, if you regularly receive documents that you need to preview and edit, you could draw a square on a section of your desktop image that is large enough to encompass these items. When you set the image as your desktop background, you will be able to drag the relevant items to this area.
Note that by initially selecting and deleting the screenshot's contents you have set the background of the image to be transparent, which allows you to set the desktop's background color in System Preferences and still see it behind the boxes and layout that you create with your custom image.