What's the ideal way to hold the controller, and what's the most efficient controls?
First off, should I use L or R for wavedashing, shielding, etc? From my understanding, you should shield with one and wavedash with the other (so shield with R and wd with L) since it makes it easier to wd out of shield. Is this true? What's the ideal setup?
Secondly, is using c-stick necessary? I never used it when I used to play, so I'd have to change how I use the controller in order to use it. I find it can be hard to use my thumb for c-stick, b, a, and jump. What's the remedy to this?
Thirdly, how do top level players hold the controller? I want to figure this all out now so I don't form bad habits and have to work out of them later.
You can WD OoS with the same trigger. It may be more difficult starting out, but past a certain point it won't affect you at all. The trick to WDing OoS properly with the same trigger is to not fully release the shield. Assuming you are holding the trigger all the way in, just barely release the part where it clicks during your jumpsquat frames, and then repress it again as soon as your character is airborne. The fastest jump is 3 frames of jumpsquat (characters like Fox, Sheik, Samus, ICs, etc.) and they are all entirely plausible to use one trigger with.
The C-stick is practically mandatory. There's a lot of things you physically will be incapable of doing without it. You simply can't do things like FF and uair on the same frame, getting full momentum in the opposite direction of an aerial, or pivot smashes, and other techniques just become wildly easier with C-stick usage. C-sticked fsmashes are also slightly quicker (you can charge with Z if you need to), and it allows you to buffer out of shield options (roll, spotdodge, or jump).
Why do you find all the main buttons to use with your thumb? That seems really weird because your thumb should naturally sit on A within immediate access to Y and B. C-stick can be a bit awkward for a while, and I still don't use it for many attacks performed immediately after jumping (it's hard to go from Y to hitting the C-stick up), but it shouldn't be too hard. Start with simple stuff like late aerials where you have plenty of time to think about pressing it or aerials after you drop through platforms (so when you push down on the stick to drop through, you can uair immediately with the C-stick).
Top level players hold controllers in all sorts of ways. The most common is also the most natural way where you simply use your thumb for all the face buttons, but some players use a "keyboard" style while others "claw" the index finger onto the controller face specifically for jumping. Keyboard style is pretty unorthodox, but Javi uses it and he doesn't seem to have any issues with tech skill. One concern people have brought up about it is the inability to use the right trigger and Z properly for grabs because you only really have your pinky near them. Clawing has a similar issue, but because you're only taking away one finger from the right trigger area, you could probably rest your controller on your leg or something for balance while pressing R and Z with your middle and ring finger. The main benefit both of these methods has over the traditional one is that you can very easily jump and C-stick at the same time. If that's appealing to you, give it a try.
One other option to explore is jumping with the control stick. I think most people would highly recommend learning with Y because it's closer to all the relevant buttons than X and jumping with the stick while trying to aerial can make a lot of things hard or impossible, but it can be helpful to be able to jump with the stick for things like JC usmashes, low immediate uairs, and other random stuff. You can learn this more as you go along though.
The last thing that is important is trigger tricking. You can remove the spring from a trigger so that it acts more like a button. This removes your ability to lightshield with that trigger, but in exchange you can powershield very easily because you will always get your hard shield out on frame 1 (you cannot PS with lightshield). This also makes it a bit easier to tech and airdodge because you don't have to worry about how far you are pushing down the trigger. You can easily remove and replace springs, so at least give it a try and you can always put it back if you want it).
My recommended configuration (not the same as the one I use, unfortunately):
L - Lightshield/hardshield, wavedash, L-cancel (make sure you learn to light press your L-cancels so they don't count as tech inputs and make you miss techs)
R (trigger tricked) - Powershielding, shai dropping (lets you easily L-cancel after quick drop throughs), teching, wavedashing (since most of your WD OoS will not be after PS, you will probably want your WD trigger separate from your "regular" shield trigger, L)
Z - Grabs, hold to charge C-stick smashes, grapples with or without an airdodge (Link, Young Link, Samus); as long as you aren't playing a grapple character, you can use Z for aerials; you can also use it for L-cancels, but idk what quirks come with that (you might do stuff like accidentally attack if you ledge canceled before inputting it whereas a light trigger press in the air won't do anything).
Y and A - Jump and standard attacks; rest your thumb across both, and you can alternate jump and attack timings easily by doing a sort of seesaw motion with the last joint of your thumb; you should be able to jump and attack at the same time or with any sort of timing in between because your thumb never leaves either button (except to press B or C-stick)
B - Closer to Y; get good at sliding your thumb from Y to B and vice versa, ESPECIALLY if you play a spacie
Alternative:
Claw your right index finger onto Y or X (doesn't matter which if you're clawing), and press Z and R with your middle and ring fingers respectively. If you can get comfortable with this, it's probably the best.