Mission file structure, editing default files

This seems like the most basic of questions, but after days of reading I'm still not clear on this.

Question is: when editing files from the game's default pbos, what is the proper way to then include them in mission files?

e.g. I'm working with the Superpowers mission. Many of the config/init scripts are drawn from the warfare2.pbo.

When editing these files, is it enough to simply place them in the new mission folder?

Is the folder structure within the mission folder important?

Will the default files be completely overwritten with the new information? Merged? Load order issues?

Or am I completely missing something about how this works?

Another example. I'm trying to apply this fix for Alice2:

http://forums.bistudio.com/showpost.php?p=1709344&postcount=21

In that case there's an edited file originally included in modules_e.pbo. But there's also a second file, alice2.sqf, which isn't in the original pbo and he says needs to be executed. This leads me to believe including an edited/fixed file isn't enough?

Apologies for my noobness, just getting started on this stuff. Any advice or links to existing guides on this subject would be greatly appreciated.