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The boxes that have the PX is the margin of the object. The Margin is the number of pixels around the object. So if you put in 20px for all of the boxes, there will be 20px of spacing around the object. If you put it in the top box, there will be 20px of spacing from the top, etc. Thats what the margin is and thats what the boxes are.
The properties is just options of that object. if it is a youtube widget, the properties will be the URL of the video and the width and height. Thats what the properties is.
You can also be on the properties tab and then click on your website background and there will be properties / options for the page (Like the page title, the title in the browser, etc.)
I hope this helps!
If you need any more assistance please let me know!