Design the site structure
Designing the site structure is three-fold, not only are you defining the folder structure of the site, you're also defining the main navigation of the site and the basic structure of the main documents. To design the folder structure you'll want to group the content archetypes into their most logical areas, be it by organisational or functional metaphors via some kind of "mind map" or "flow diagram". From there you'll want to establish a hierarchy of importance among the areas, so card sorting might but be a good option, which will lead into the main site navigation, just remember not to fall into "the myth of Seven, Plus or Minus 2".
For designing the page structure, I'll leave that to the W3C
"To determine if content is structural or presentational, create an outline of your document. Each point in the hierarchy denotes a structural change.
Use structural mark-up to mark these changes and presentational mark-up to make them more apparent visually and aurally. Notice that horizontal rules will not appear in this outline and therefore are not structural, but presentational. Note. This quick test addresses chapter, section, and paragraph structure. To determine structure within phrases, look for abbreviations, changes in natural language, definitions, and list items."
