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I created an entire system, and it seems that I put it in the wrong place. Is there a way to change the coordinates of the system without recreating the entire thing or am I just boned here?
You can move it with the pointer tool. Select the pointer tool from the menu, then select the system on the map. Then drag it around. For more precision, you can hold down the x, y, or z key to restrict movement to that dimension.
Alternatively, you can select the system, open up the properties window, and manually enter its coordinates.