Global variables are one of the first things you learn to reduce when learning good programming practices. They cause a number of problems. They can make debugging harder because any section of the program's behavior may depend on the global value. It is also hard to tell what part of the program might make any use of the variable. Any variable's scope should be confined to the context in which it is used and not be accesible by parts of the program that shouldn't be using it.

Can global variables be avoided altogether? Yes, essentially. There is a programming paradigms called functional programing where global variables can't change value once they are defined. Learning different programming paradigms like this is helpful in learning good coding style.

I am not sure how helpful I can really be in describing the best practices for organizing code here. Learning how to structure code takes a while and requires a fair amount of reading and practice with things like design patterns and reading real world code.

From experience talking to people new to programming with Mathematica and other similar languages, my best advice is to write as much of your code as possible using stateless, pure functions (https://en.wikipedia.org/wiki/Pure_function). That is, to write functions which take input and then produce an output which only depends on that input. These functions should not use any global variable. If they do use a global variable, make that global variable an argument to the function instead. Your program then becomes the process  of taking the input and running it through these pure functions to produce the result you want to see.