I need to place a lower third I made from another program into the storyline. The background is black but I need the white text of the lower thirds to show only. Is there a way to make this transparent?
The effect you want is called Chromakey and Photostory does not support this.
However if the Lower Third is static ie an image, export it from the original program it was created in as a png file with transparent background and import this.
Alternatively if the lower third is only text use Titles in Photostory to create it.
To animate an image or title use Keyframes - see the installed PDF manual under Help.