When you want to placxe a hole/gate, go back to the map of Sirius. double click with the left mouse button on the system you want to add a gate/hole to. right click where you want the gate/hole, and select either jump gate start or jump hole start. (IF you can't get it exactly where you want it go back in editing mode later and move it. Either use the wheel on your mourse or the + and - on your numpad to zoom in for greater accuracy)
Now back to the Sirius map, and do the same with the system you want to connect it to, but this time choose jump gate end or jump hole end. A window will come up with options. If you have made a jump hole you have the option over what color it is, if you have made a gate you have the option whether you want a normal gate or nomad gate.
Now choose the reputation of the route, and you're finished.