Courses that are set to Windowed will be deployed via a pop-up window. 

Courses set to Embedded will deploy in the same window as the LMS. 

Courses set to the windowed option could be challenged with browser pop-up blockers and could experience issues when being viewed on mobile devices. 

Courses set with the Embedded option will help keep the LMS window active when viewing on a mobile device and wil by pass browser level pop-up blockers.