Hi all, i am new to zencart and looking for some advice

I have inherited the zencart website its updated to 1.3.9dand it has the classic green template... minor changes, eg header image , royalmail shipping modules, new button set, uk counties, this is what i am aware of or the changes i can visibly see,

here is were the fun starts cause there is no custom folder, so could some tell me what custom folders and files i need to install so i wont lose the changes if i need to upgrade in the future
( yes i have used the search function and read the tutorial on creating custom folders) but i dont understand what files i need to put in them.

any help in resolving this matter would be great as i dont want to start again from scratch

regards
dave