This is a 3 part series that discusses about Publishing features and concepts surrounding it
http://sharepointchick.com/archive/2011/01/12/sharepoint-enterprise-features-functionality.aspx
Another article that discusses sharepoint publshing feature
http://www.thesharepointmuse.com/2011/12/lesson-learned-when-you-need-to-use-publishing-in-sharepoint/
Finally, I would still suggest read this book
Professional SharePoint Branding - by Randy Drisgill.
It has all the information you need concerning the SharPoint publshing infrastructure.
Concerning Information Architecture for your intranet go through this following links
http://www.harbar.net/presentations/suguk_ia.pdf
http://blogs.msdn.com/b/joelo/archive/2007/03/16/information-architecture-and-the-information-architect.aspx
http://www.cmswire.com/cms/information-management/5-critical-steps-to-sharepoint-information-architecture-planning-014188.php
This is a Microsoft case study of MOSS 2007 information architecture in depth
http://go.microsoft.com/fwlink/?LinkId=91053
Besides, the above links I recommend the following quick points before you proceed
Define what before how.
Do a great deal assessment on what kind of organization, the size of the employees , departments and divisions , current processes , modes of offline employee collaboration and create a solution roadmap on sharepoint and how to leverage the best using an intranet build on top it. This "what" should be as descriptive and clarity must reside before you proceed on "How" to implement them.
Use only whats needed.
SharePoint comes with multitude of collaboration features like document sharing, blogs ,wikis, bi ,team dsicussions, search , social sites etc. A majority of intranet implementation on sharepoint somewhat drifts towards this feature creep and adds unneccessary site templates and enable features which are either not used or have no real requirement for the business. Keep things simple and ensure only minimum required features are present per site.
Document everything.
The title says it all. Document every corner of the farm including services, servers , roles , web applications and site collections , site collection administrators , features activated per site , hierarchy of subsites ,etc. This document will become an indispensible resource once your intranet grows.
