There is a maximum of one working runway per island. On the official islands it always runs north-south, I don't know if that is required on user created islands but I suspect so.
If you want an aircraft to take off from a non-working runway, how you do it depends on whether the player will be watching. If not, it is easy to fake. If he is, it is hard to script (setVelocity is the key command) but could perhaps be done, if it hasn't been already.