This is going to be hard to explain/ask:

With all these scripts, how do you know to put so many "td"s and whatnot, or where they go? How do you make these codes work? Like, where does it all stem from?
I don't know if I got my point across, but with all these scripts being added all the time, it got me wondering how people know what to put to make them work.
How can I learn, if that's possible? How do you make them?

HTML, and scripting takes time and practice. You'll have to learn it slowly from scratch and basics. It's really fun and simple once you get the hang of it. I suggest you ask a friend who knows alot about it, or google some tutorials about how to script, and HTML, etc.

When I come up with codes or tweak others' to help them out, it's usually just through trial and error. Another way is to study the codes that are already provided. It gets easier in time, as long as you practice like Tung said. Once you understand HTML/CSS, you'll be able to read through MySpace codes and tweak it yourself in no time.