You should be able to do this in ImageJ. The first problem will be that the field of view from each magnification is different. The next problem is that the resolution will be different from each imaging device. You can figure out the distance per pixel of each image by measuring the number of pixels between two features that are the same on each image (like the edges of the cell). Then you can re-scale the images to have the same distance per pixel. Then use the overlay tool to merge the two images.
You can also hand scale one of the images in ImageJ. The overlay tool is quite versatile. Check out this page of the ImageJ User Guide. http://rsbweb.nih.gov/ij/docs/guide/146-11.html