I have purchased an animated lower third that can opened using After Effects. What I want to do is to be able to create diffrent lower thirds with diffrent names (transparent background) and render each one as a quicktime file to be able to just put into my premiere pro movie when I need it to be shown. The question is: How do I export After Effects animated lower thirds into Premiere Pro CS5 with a transparent background, so it will just show the animated lower third. Any answer would be highly appreciated.
You need to render the file with an alpha channel. You want to set the render up as Millions of Colors + Alpha, Straight Alpha and then use a codec that supports alpha channels. Depending on your system this may be ProRez 444 or Animation Quick Time, Or a png sequence.
Press F1, go to the help files and read the section on rendering and output.