I recently stumbled upon one of the best articles on the HTML structure of Squarespace v.5 wireframe developer template. Even if you are using one of the other squarespace themes / templates, this article will help you better understand how tweaking the various elements via css affects your layout.
And if you are not familiar with the Squarespace Wireframe, go grab a copy of the pdf here. Print and staple to your wall for easy access!
You may also want to check out our master list of Official Squarespace Resources as well.