[Typo3] Newbie question for a complex site

[tapio]

> 
> I'm thinking of putting a ###SECTION_CSS### tag in the HTML template and 
> using that to insert the appropriate styles for each section. Is that 
> the best approach?

CSS Style Content +  HTML/CSS Styling and you can powerful control the 
the content and layout. Altering constant for CSS you can easily change 
the CSS-file. Or use cssselect plugin. You can have a list of CSS-files, 
which you want to use in each section.

> Navigation: There's a horizontal menu across the top of the content with 
> a link for each section. Then there's a menu on the left hand side with 
> the page tree within that section. I'm not sure how to organize the site 
> to get both menus running automatically. Should I make each section a 
> "site" or is there a way to say "create a menu from this point in the 
> page tree down"?

At least you can set that the first level menu items will not be printed 
and the menu starts from second level. I have used menus, where the main 
  menu has just items on the first level.

look at from here how to set menu items so that they would not be 
printed at all
http://typo3.org/documentation/document-library/doc_core_tsref/TMENUITEM/

Sub-menus are in a different menu. Typo makes this automatic if you 
define menus correctly.