Is it possible to get more control over my global variables white space?
The indentation of their includes gets knocked all whack when i view page source?
Just leave any whitespace that would have been there in the original template. They drop into your template just as they are. So paste in the variable code just as it would be in the template - with tabs etc.
Am I able to edit them as text files the same as the template files?
No, but you can if you use a program like Mountee (but it’s only for Mac).
On the same note, should I be using a global variable in the same what I would use a PHP/ASP include?
You have three options: use a global variable, a snippet or an embed. Use the global variable if the code is just html/css/js. Use a snippet if there there are basic EE tags in the code, and use an embed is you have channel tags etc that need to be processed. (That’s a really basic and inaccurate summary of each. See the docs for more precise info.)