Unfortunately it does make a difference where the lines go.
If you're standing in front of the plane and look down behind the engine, here's the setup: 1) The line on the far right goes to the remote needle valve. 2) The line in the middle is the "fill" line and that's where you put the "plug" 3) The line on the far left goes to the pressure fitting on the muffler.

Line #1 draws fuel from the tank Line #2 Used to fill only Line #3 Pressurizes the fuel tank and also acts as a "full" gauge.

Hope that helps. There's ton's more information about the NexStar on http://2ndrcflightschool.com/tipsandtricks.htm .