You can use the File->sync images ... menu option to synchronize two or more images, so that when an operation is performed on one image (e.g. change of colormap, contrast/bias, pan, regions, scale, wcs, zoom), it also is performed on the other image(s). First, choose the operations that you want to sync. Then choose the images that should be kept in sync.
By default, synchronization is reciprocated: a change in any image causes the others to be synchronized. Synchronization can be configured one direction only by unchecking the reciprocate option. For advanced use, the JS9.SyncImages() and JS9.UnsyncImages() public API calls are available programmatically or from the command line.
This demo displays Chandra, Galex, Spitzer images of the colliding galaxies NGC 2207 and IC 2163, synchronized on region operations. The region screen sizes differ because the image scales differ, but their wcs sizes are identical. Move a region around to see updated region stats for all three. (You can, of course, use WCS:reproject to display the same scale and orientation.)
This demo displays three energy cuts of the Chandra Kes 75 supernova remnant. The first two images are sync'ed to changes in all operations (colormap, contrast/bias, etc.) The third binned image is sync'ed to all ops except zoom. Change a region to see all the energy plots get updated, or change the colormap, contrast/bias, scale, etc.