I'm not very sure which method of organizing a settings page (Wordpress):
Option One:
Header - Content - Footer
Example:
Header
Front Color:
Background Color:
Background Image:
Option Two:
Colors - Images - Fonts
Example:
Colors
Header Background:
Content Background:
Footer Background:
Which option is more efficient and extensible in the long run?
(Basically, the dilemma it's "page sections" vs "HTML elements)
Option Two- Minimize the number of major categories Colors, Fonts etc. You may end up with four or five categories, rather than creating a section for each element. Header, footer, left sidebar, right sidebar, blah blah blah. You can continue adding elements as you want to make settings more precise. Visit wordpress.stackechange.com for more insights
You mentioned a simple folder problem. Fixed hierarchies will often result into lost users. If your users are familiar with Wordpress I would use the way Wordpress already uses. This way you provide an already learned pattern. Otherwise you could try to stuff all features on one screen until it's getting crowded. Improvement: less clicks and everything on one place. I can't tell you what of your mentioned orders are best, though.
If you want to make it fussy perfect you might need to check what changes are done most often. That could be the top two features, e.g.: 1. Change Header Background 2. Change Body Font and Color 3. The rest
