As far as I know, you can't get the game to run in a standard window, only in the full screen mode. It is possible to access other windows via Alt-Tab and Ctrl-Esc and maybe other magic key combos. If you have 256 meg memory, you can run a reasonable amount of other stuff concurrently, including a browser and email/connectivity software, although some items, such as sound, may be problematic (i.e. available only to SMAC or ...) and instability may be more likely the more resources you are using.
As to the screen resolution, you might want to be more specific about your problem. I believe that SMAC uses either of 2 resoultions, 1024x768 and one lesser, either 800x600 or 640x480 but probably the 800x600. I think that if you are already using one of its supported resolutions, it will go with that, otherwise (I would hope that) it would go with the highest one less than or equal to your current resolution. There is a line that can be entered into the file Alpha Centauri.ini that will specify a resolution. I don't know what that is, but I imagine that you can find it in a readme.txt kind of file or else in another thread on this subject. The .ini entry has definitely been mentioned in this forum, so that knowledge is out there. Of course, you may be talking about something else. . . .