You can't as far as I can see... Chroma-Key is only in the video editing software like Movie Edit Pro and Video Pro X. It requires multiple tracks for image objects.
Though the main info page shows only storyboard mode, a google search for photostory + timeline found a PDF file 'Getting started: MAGIX Photo Story' which indicates the program has a timeline mode like the other Magix video editors. An illustration shows at least four tracks but it's not clear if they are dedicated to images / effects / titles / audio.
I'd assume they are general purpose in which case track 1 would be the background image to show and track 2 (or any higher number) would have the object with its plain green screen background. The remaining question is whether PhotoStory provides a chroma key effect. Have you searched for "chroma' in your PhotoStory Help file?
Yes, there is a Timeline Mode in the PhotoStory software, but each is dedicated to a particular media.
Track 1: Image Track (Photo, Video)
Track 2: Audio Track (audio from a video file will show here)
Track 3: Text Track
Track 4: Audio Track (narrative, music)
That is the gist of the Timeline Mode. For chroma-key there would need to be at least one additional image track, so a layering can be established. Also, there doesn't seem to be any information on chroma-key effects for the PhotoStory software.
My recommendation would be to try out the Movie Edit Pro software which would allow you to still import and use all the photos (in a identical way as PhotoStory) as-well-as many new effects which require multiple tracks for layering.