For ear training, you can say that nat 9 prefers whole tone over altered or diminished, nat 13th prefers diminished over altered. Basically, if you know the what alterations your scales contain, you'll know what to use.
In the end, when you know them all, your ear takes over and you can play some "illegal" stuff and make it sound good. Whole tone on G7b9#9 for example. Or half whole diminished on G7#5. Good players can make breaking the rules sound good. But you have to keep to the rules in the beginning to train your ear so you can break them