You can work the clutch line in place but it is definitely easier before you install the engine.
You will need the tunnel cover off and the seats out of the way.
In the front the clutch line follows the same path as the bake line.
In the rear the clutch line goes between the subframe and the fuel tank and then up between the engine and fuel tank.
As you work it through the frame it will straighten some of the bends so once it is in place you will need to correct the bends. It is easy to do this with your hands.
This is also a good time to place the two heat exchanger tubes into the tunnel.