CSS should be used for formatting your document. This is really a question of howe clean your HTML markup is, but it could affect your PHP performance, in that using CSS classes properly might reduce the formatting markup you have to generate and transmit.
what properly goes in a functions page
Functions pages act as repositories for 'general' functions that are used throughout many other pages. This also allows you to group related functions in a single file for easy debugging.
what is the speed penalty of a giant functions page vs lots of separate pages
That's a hard call; giant pages take longer for the Zend engine to parse, while shorter pages take less time to parse, but require more calls to the underlying operating system to fetch.
Essentially: If you're dealing with a LOT of code (thousands of lines) the, it might be a good idea to break it up into several files if you only need specific, well defined subsets for individual pages. If you have to include every single smaller file in every page, you're still processing the code AND waiting on the operating system (bad idea.)
the merits of config pages
As mentioned earlier, config pages play a security role. The other thing they do is allow you to put a lot of related settings in a single page, so that you don't have to sift through functions to change settings. If you plan to distribute your application, it might be a good idea to seperate your config, because it's a lot less daunting to edit one file than digging through many filled with functions.
should pages be many small interlinked or larger self-contained using ‘?xxx’
I'm trying to decide for myself on this one. The GET variable version allows easier access to the site, at least programatically.
does one have to start with a schema or can it develop as you go
If your code is ever going to be reviewed at a later date (by yourself or anyone else) PLEASE, PLEASE use a well documented design schema.
Plus thinking it through will often provide you with a better understanding of exactly how to accomplish certain tasks before you get there.
I've tried many times to just blow through from the bottom up, but trust me, the top down is much better.