How do I make custom maps?

[Taz-in-Space]

To expand on what Tesco said, the reason for generating a map in the game program rather than the Map Editor program is the Map Editor's map creator is NOT truly random. That is the map generated by the Map Editor's generator will ALWAYS produce the same map if identical settings are used.
The game program's map generation seems to be truly random...
Other things to watch out for:
1) Do NOT delete an entire system without deleteing all contents of that system! You will get the contents of the deleted system in SOME OTHER system elsewhere on your map.
2) Remember to be extra careful with warp points. A normal warp point is TWO WP items - one for each system.
3) Be careful not to load a map from one mod into the editor of another mod. Especially if one mod uses modified planet sizes or other such changes. Ex: Extra-Huge planets