Overrides folders...

I am trying to customize my template and at the same time change some things here and there. But I am curious as to which files I need to copy from the default template.

In my includes > template folder I created some folders:
Buttons (which contains the buttons I am using)
Common (it's EMPTY what am I supposed to do with it?)
CSS (it has the files I copied according to the tutorials found in here)
Images (They have my template Images... background, header, logo)
Sideboxes (what is this for?)
Templates ( what is this for?)
this is how it looks
includes
/templates
/CUSTOM
/common
/css
stylesheet.css
/images
/sideboxes
/templates
template_info.php

Here is my question:
As I edit PHP files where do I save them? Should I create a folder where I found the original PHP file and save it there?

Some tutorials ask me to change a file from the COMMON folder but mine is empty, should I copy these files from other COMMON folders and put it in mine?

Ok guys I have found the answer to most of my questions I still don't know what is the purpose of the COMMON in my template folder...
Whenever I need to edit something from the COMMON folder should I copy it from the template-default and paste in my template?

Thank you :)

Yes. Copy the file from template_default/common, edit it, and save it to YOUR_TEMPLALTE/common.

Thanks Stevesh
Do you happen to know how to change the font color of the Home/log in header and footer?

Look for navMain and navSupp in the stylesheet.