So, I've got a few problems with my playing.

First, and I'm not really sure if this is a problem or not, but when I hold my pick, I hold it with 3 fingers, my thumb, pointer and middle. From what I've seen, many players hold picks with two fingers, but I'm just not comfortable with it. Is it really even a problem?

Secondly, when I play, I often play with my left thumb pressing up against the back of the neck. Usually it's not a problem, but sometimes it starts to ache a bit, usually when I'm reaching for the lower strings. Also from what I've seen, other guitarists don't do this, and it seems like it might impact my left hand mobility. So what should I do with my thumb?

Uh. So I probably have some other problems, but can't think of any right now. So any advice would be appreciated. Thanks.
Terrible even.
I've heard of someone famous doing that, like EVH or James Hetfield or something. I don't see how it could hurt you for beginner to intermediate playing. But whether holding a pick like that and playing crazy shred stuff is healthy or possible, I don't know. If I were you, I'd correct your technique now before you're too set in your ways. Just sit down with a metronome, turn it to really low BPM, and get your muscle memory on.

If your thumb starts to hurt, you definitely are doing something wrong. The amount of pressure it takes to fret a note is really small. You should keep your thumb in the center of the neck, but just relax. Get out the metronome again, set it really slow, and focus on using the least amount of pressure you can while fretting.

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I used to hold the pick with 3 fingers aswell. It feels more relaxed at first, but then I realized I had very little control over the angle of the pick. This can become a problem when you speed up.

BrokenBricks has the right idea for the second "problem" - I put quotations because I think of them as obstacles, not problems. Read his advice.
There's generally two ways to hold the neck and position your fretting hand thumb, its best to use both and get comfortable with alternating between them depending on what your doing.

The first is the classical position, where the thumb stays behind the neck and the fingers stay curled and parallel with the frets. Its good for faster playing and scales.

The second is the blues position, its where the thumb is wrapped over the top of the neck and the fingers are diagonal to the frets. This is good for bending and vibrato.

I find the classical position to be harder so i mostly stay in the blues position. If you only play classic rock type stuff, you wont even really need the classical position. Its really only necessary when your playing high technique stuff like shred or classical. Or when your playing complex chords that require you to stretch.
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I hold my pick the same way Ace Frehley does.
You'll have to watch videos of him playing to understand what I mean, because pictures don't really show you how he picks.

I do a lot of things Ace does, now that I think about it.
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Steve Morse plays with three fingers, I do too.

you can't see it to well here

Is that the same guy who developed carpal tunnel?
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Is that the same guy who developed carpal tunnel?

Yeah, he anchors though, which might explain it.
adding the third finger increases muscle tension in your hand and arm. short term it isn't hazardous, but after excessive playing for years with the 3-finger grip, the damage will become obvious and you could do some serious harm to yourself. The less tension, as i've said many times, the better your playing will become.
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Bitches be Crazy.

Thanks for the advice guys, over the past couple days I've transferred to holding the pick with two fingers, though I still have some work to do because it's not yet quite as comfortable as how I used to do it.

Guitarninja, thanks for the info about the different positions. I've started using the 'classical' position quite a bit, and I'm amazed at how much easier it is to reach lower strings, especially on higher notes and with my pinky... which is a really good thing considering it's already hard to hit higher frets with my pinky, because it's bent about 15 degrees.

Despite all this though, I'm still having trouble with my thumb. It seems that no matter what I do with it, I always end up pressing against the back of the fretboard. When I play something that moves position, (chromatic scales for example) my thumb doesn't move with the rest of my hand, it just sort of locks in place. Also, when I need to reach for something on a low string, it feels like I need that pressure to do it. It's probably just habit, and I know I need to figure it out slowly and break it, but any advice would be great.
Terrible even.
Keep your thumb at the back of the neck, it's the right position. To be honest, most guitarists you know use wrong technique. Look up classical left hand positioning and you'll be fine. Also search around for a post of mine about nerves and how they work with your wrist.
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