Merging in MM seems to works better than merging in imaging software - not sure why and you need very little overlap between images.
AFAIK MM merges purely from the calibration data (not the image itself) and splices at the "boundary" (route) of one of the maps. Note that there is a bug which causes narrow (white) gaps to appear with very long East-West edges.
By "imaging software" I presume you mean a utility which automatically merges (optically) photographs to produce "panoramas", etc.? Personally, I just use the "Print Screen" key (to put the grab into the clipboard) and then paste into an image-processing program. Mine is an ancient version of Paintshop Pro (which was free on a magazine cover CD) but there should be other suitable free packages. It's normally easy to manually splice together 4 or 9 grabs and maybe many more (I believe later versions of PsP can handle images of at least 100k x 100k pixels). If your monitor isn't very large, you may be able to send the video to an HDTV (1920 x 1080 pixels) to reduce the number of grabs.
The procedure I use is:
"Print Screen" : then in PsP "Paste as new image" : "Enlarge canvas" (for the first screenshot). Then zoom in to a degree where the image is recognisable at pixel level and move an edge (where you plan to add the next image) near to the centre of the screen.
Then for each subsequent grab, "Print screen" : [ If necessary, "Paste as new image" : Crop as required : "Copy" ] : "Paste as new selection" into the first image window and drag to align the map detail. If it doesn't align perfectly you can probably "Undo" and try again.
I find this process much quicker than calibrating individual map sections (unless they have a very closely-spaced Reference Grid overlay).