I've tried and don't like the three line set up. That just me though. Leave the third fitting plugged and get a fueler valve and use the 2 line set up. Hook this in line with the carb. In the GP cub you should be able to see the fuel tank to know when to slow down fueling and let a little run out the muffler.

Acually I've build both the 40 and 60 GP cub and found that enlarging the opening around the engine to be the best way to fuel it, unless your planning to enter the plane on anational level no one would ever notice. Enlarge the cowl around the carb enough the reach the carb nipple and fuel line and grab it with a pair of hemostates. Of course I'm running 4 strokes mounted sideways. It kinda sounds like your running a 2-stroke upside down in which case go with the fueler valve. I did that on my first 40 sized cub and put the fueler valve right smack in the middle of the top of the cowl were the real cub is fueled