Paying attention to your body is a skill. Alot of people do have some degree of innate proficiency at it, but it is something to be done deliberately and practiced, and with enough deliberate practice you will eventually do it automatically with high mastery. You're still a child, so you have plenty of time to develop this skill :)

May I make a suggestion? Instead of just water breaks... take breaks. Get up, stretch your arms and hands, your neck and back. Walk around for a few minutes, even just in place. Drink your water.

You'll save yourself a lot of future pain.

I'll definitely keep that in mind. I'm planning on using a standing desk, does that do any good?

It certainly can, but you have to remember to monitor your posture so you don't slump. Good luck!