There is one effective way to edit a map:
Use the map editor to make the systems, place the planets, and everything else BUT the warp points.
Save the map and load the map and start a game with it, with tech setting set to high, enable save map in game, enable cheat modes, and load up your race as the only one in the game.
Start the game, and click yes when it asks you if you still want to play the game.
Build a stellar manip ship, and warp away.
After you're done, save and finish!
