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The developers have gone to great lengths to map and electronically recreate the Milky Way to scale to make the game as realistic as possible.
Yes, the modules all have a position in or on the ship, and some calculations are done based on your armour to decide if there's any penetration at all (which gets more likely as your armour gets beaten up), then how far it's likely to penetrate and which modules are along the path of that penetration and might take damage (there's several more subtle rules, but that's the broad strokes). You can use the Galaxy Map to navigate through the Milky Way galaxy.
The System Map displays a system's layout and information.
Most of the action will take place within the human populated core systems of the major factions. It's where powers compete for influence, resources, territory and control.
The Elite Dangerous page on this wiki has more information. It will be expanded with ambitious features such as Atmospheric Landings and on-foot and out-of-ship activities also known as Space Legs.
Such as FPS combat, walking around and boarding ships, walking in stations and walking and driving vehicles on entire 1:1 scale populated living planets, multi-player crew and player executive controlled capital ships.