You need to drag the systems to where you want them. This allows you to set the map up however you want. Click the help button at the top and the side panel will explain how to drag them. I've copied the key section here for quick reference.
To move a single system, just hold shift and
drag the system using the mouse. To move
multiple systems, firstly use Ctrl-Click to
select several systems or drag a box around
them, then hold shift and drag one of the
selected systems. Other selected systems
will also be moved by the same amount.
To deselect one of the selected systems use
Ctrl-click again. To quickly deselect all
selected systems, drag the mouse in a clear
area
The Keypad numbers can be used to move
the map in eight directions. The Keypad plus
and minus can be used to zoom in and out.
Be aware that unlike the older Galactic Map,
no changes to system position are saved
until the Save System Positions button is
pressed. This allows experimentation without
commitment. Or you can use the Save System
Position option on the right-click menu
Steve