Jon:
You have two openings in the wall, and they do not operate with each other. One work around is to create a small piece of wall that is the width, height and
depth of the niche, place the window into this wall, and move this wall into the niche. This way, the niche operates on your main wall, the window operates on the wall inside the niche. If you posted some images of what you are trying to accomplish, then someone might have a more efficient or simpler way of getting this done.
If you plan to ask more questions here, please create a signature with your ArchiCAD version and platform (see mine for one example).
HTH
David