The best and most functional method is to have it going straight out from the receiver so that it is not folded back, or wrapped around anything (especially wrapped around something). If you can figure out a way to do that, then you are good to go. Folding it back will reduce it's effectiveness somewhat. Passing it through a pushrod tube is a good idea, as long as it's not metalic. In fact many models provide a tube to pass your antenna through to the rear.

If you pass it through a tube, tie it off somehow so it does not snake itself back into the fuselage and form a ball, which is what it would do if you didn't secure it somehow. You can put a very small tie-wrap on the end as it exits the tube outside the rear of the aircraft if you wish, or some other method of prevening it from snaking back into the fuse. Vibration does that.

JUST don't cut it! Leave it the same length as it was when you got it new.

As you suggested, run a tube so it comes straight out the rear and tie it off and let the bitter end dangle back there. It won't hurt anything.

CGr.