Jeremy Miller has an awesome series of posts on starting up a new project from the ground up. He is covering all kinds of things I had questions about when I was first trying to get started and filling in gaps.
Seems like most tech articles make too many assumptions about the consumer's experience and so don't include even simple considerations like file structure, namespace conventions, and so on. Jeremy doesn't have this problem at all and instead is a great teacher.
Check 'em out at http://codebetter.com/blogs/jeremy.miller/archive/category/1315.aspx
While you are there, read his other info...great wisdom.
M