In the JEmbedAll configuration sections (go to Joomla administrator / Components / JEmbedAll / Configuration / Configure pop-ups) you can define any number of pop-ups, each one with its own width, height, the cookie time (if you use cookies this set the time until the pop-up will appear again), the type (session or cookie), the template, the time until the pop-up closes (by itself), the link of the image and other details you need. You can add an image, a Flash file or an Joomla article inside the popup. Only one of them can be set active at any given time, but you can get all of the inactive when you don't need them anymore.
You don't have to embed the pop-ups on site in order for them to appear: make one of the active and it's enough. The JEmbedAll plugin will show it.