Hey, sorry it took me so long to reply back. I didn't have much trouble making maps...it takes about 30 min to draw one out on graph paper, then another 30 to 40 min to write a file up. Then it takes another hour or so to test it...going through the sector, trying NOT to come into contact with the other carrier before you've mapped the whole thing out; Unfortunately, however, I can't think of an easier way to do it.
I don't know if you're aware of this, but the CIC has a Universe Maps section which contains the 11 Armada maps (below the big universe map). I was able to create the first two maps using the JPGs there. Since the maps were designed with the game in mind, they might be better suited than some of the sectors in the big map. Vega works quite well, but Enigma's got a row of about 10 systems (Pournelle, Piper, Cabrea) along the top half which never comes into contact with the rest of the sector; you'd have to either change the map or just ignore those systems entirely. Anyway, if there was a map selection screen or random chooser, it would probably up the playability several times over. Hope this helps.