NOTE: We have done this with CRM 2011 on-premise. We don't know if all of this applies to CRM Online.
The basic layout of the CRM 2011 web application is configured in something called a "site map". This is an XML file that contains a lot of settings that CRM uses to build the navigation screens and menus in CRM.
You can edit this site map to customize the look and feel of CRM 2011. See this Microsoft article on how to do it:
http://msdn.microsoft.com/en-us/library/gg309424.aspx
As this article mentions, you can also edit the "site map" using a tool called Site Map Editor:
The same article also mentions another tool to edit the "site map":
http://sitemapeditor.codeplex.com/