I doubt that you can do it in a completely satisfying way, but here is a half measure that at least lets you have some of your desktop available at the same time as the game is visible.
Set your windows default resolution to something greater than 1024x768, for example 1280x1024. Run 2 copies of SMAC/X (which will reset your view to 1024x768). Close 1 of the SMAC/X sessions (which will reset your view to 1280x1024). You will be left with SMAC/X running in the upper left corner of your screen and a (backwards) 'L' shaped area of desktop. IIRC, SMAC/X will be locked in the upper left and not be resizable; it will probably be running in an 'always on top' sort of mode (but maybe not) and it may be a tad small depending on your vision and the size of your monitor. OTOH, it will happily go about its thing even if you are working in some other area of the desktop, so you could let Yang fly 150 NJ's over your territory and only give them half an eye while you did something else.
One can probably do something similar with a starting point of 1024x768 using SMAC/X's lower resolution if you specify it in the .ini file (or even combine the low resolution with 1280x1024 if you want a higher percentage of the screen in desktop mode.
I had been hoping to be able to run SMAC/X and the regular environment on separate monitors, but that didn't seem to work for me; SMAC/X seemed to come up on both monitors regardless of the monitor configuration I was using. I had the impression that this was possible somehow, but perhaps that was only in the other series of Windows (Win95. 98. SE, ME, ...). This method was sort of a consolation prize, but not a really good one for me - using the Alt-Tab, Ctrl-Esc, the Windows key, etc seem to work better for me.