Partly by hand, partly through the Edit Mode.
Relatively speaking, it's not hard, but you need creativity for it.
Download a couple of System maps and see how they do it. BanzaiZap maps are good, and relatively simple (some contain AI ships, I suggest you stear (sp) away from them for the moment). But good though.
A System consists of a System Plugin (you seem to require a seperate one for GalaxyCharts, but please consider one through Foundation as well!), a system map/folder/directory in scripts/Systems/ and then 1 or more subsystems. All named <<SystemName>>#, placements (that you generate with the EditMode) are called <<SystemName>>#_P
If you have specific questions, make sure you ask (normally, I might have gone deeper in my explanation, but my brains are going into sleep mode).
And this basicly is it, since all systems share the same structure you can mostly copy and paste and change things to your liking.