As a rule, it's usually better to route the antenna, at least a few inches or more of it, outside the plane. A lot of coverings have a metallic layer in them that will block the reception of the signal if the antenna is completely inside the plane.

The easiest way to run an antenna wire through a plane is to pick up the 1/8" tube for a throttle CABLE and route it through the plane to the outside with as few bends as possible. Try to keep all your bends shallow to prevent getting hung up when you are pushing the wire through the tube. If the antenna keeps getting hung up, wipe the wire down with a paper towel that's got a lot of Windex or WD40 on it. You will want the wire to be a little wet with whatever you use for a wire lube.