Re: I've looked and looked...
I don't know if this is the standard way of doing it, but it works.
After you save your map, go to: C:\Program Files (x86)\Steam\steamapps\common\Cortex Command\Base.rte\Scenes
Then, open the file that is named after your map in notepad:
Add x and y values under the location (something reasonable)
After that, it should show up on the map.
Disregard this post. The one below is better