The minor scales can be confusing to keep track of. In fact, all scales can be confusing until you sit down and figure them out. However, there are reasons they are the way they are and perhaps it's more important to look at those reasons than try to beat them into your head, especially the harmonic minor. The reason it's called the harmonic minor is that it's adjusted in order to provide the harmonic necessities of what our ears want to hear. Interestingly, it's not the chord of the root of the scale that's at issue here, but the V chord. What happens is the if you were to play in the other common minor scales, Aolian and Dorian, let's say A minor, and you want to create the standard dominant tonic tension and release, you'd run into trouble. If you play the V chord, E, in either of those scales, that E chord is also a minor chord and the resolution from Em to Am is not all that satisfying. In fact, if you go back and forth, it can sound more like I minor to IV minor than V to I. So, what they did was take the V minor chord and raise the third to make it major. In conjunction with the 7th degree, then we get our old friend the tritone between the 3rd and 7th (in this case between G# and D) which provides the tension that we want to hear as it releases to the Am. Try it, it works. Then, the next step to it is to play that V chord as a scale, with the raised third. There's your harmonic minor scale! It's not a scale that gets played much on the I chord (over the Am), but it gets played a lot over the V chord.
What does this all mean? Well, I always tell my students to concentrate on playing chords, especially triads, rather than scales. Scales are static and when you are running up and down scales you aren't really going anywhere. Chords, on the other hand, always state a harmonic context and give you a sense of where you've been and where you are going. It takes a bit of a readjustment to start thinking this way, but once you get it down, you'll discover that your solos will have a much greater sense of direction and become a lot more interesting to listen to. Jerry knew this in spades, as he got it from listening to the jazz players. When Trane and Miles were playing over modal tunes, which can have 1 chord for a long time, they were still playing bebop changes, which gave their solos a very strong sense of tension and release. Jerry and boys ate this stuff up and really got it. Most rock players will just run scales and their solos get boring pretty quickly because they don't really go anywhere. So, banish scales from your mind and think chords, win friends, influence people and get all the chicks!