knightmagic,

Either way works.

I have some planes with the antenna coming outside (some out the side and some out the bottom) and also some with the antenna completely inside the fuselage. They all work fine. Sometimes the end of the wire sticks out the back when the fuse is shorter than the wire, just let it stick out DO NOT cut it off

On my Twist I had to run the antenna wire out the top in front of the canopy. It was the only way to avoid the radio interference caused by the long servo extensions inside the fuse to the tail mounted servos.

Hope this helps,
Phil in MN[8D]