mapping gpio pins

Firstly, my thanks to those who have helped me with my problems in startup/shutdown questions. I think I now have the hang of it.
What I am still unsure of is where I find the relevant files to be able to change and/or enable/disable gpio pin usage.
I have no problem using putty to get at the file structures but do not know which folders & files are the ones I need.

Any help would be great