A Popup is a seperate browser winder that pops up when you load a page or click to open a link in a new window.  You will then see a seperate window open with new internet content.   You can resize, close, or browse in a popup just like you do in the main browser. 

If you would like to close the content in the main browser and just continue browsing the new content you may click Open in Main Browser.  You will then close the popup and transfer the content that was in the popup into the main browser.  This can be very useful for sites that launch their main content in a popup.