Pop-up displays on the screen in front of the window you are looking at, the pop-under is more of a window that is created and you can see on your taskbar, but you won't see it until you close or minimize your current window, or click on it directly from the taskbar
A "pop-under" is when I stick it into the toaster. A "pop-up" is when it's done. Oh wait a minute...I'm thinking of pop tarts. My bad....sorry.
Pop up is the advertisement window that appear on top of your main browser window while pop under is an advertisement that appear underneath the main browser window. Both popups and popunders are annoying to visitors and will drive them away from your site.