Here is a high level overview of the files located in a site  definition: http://heathersolomon.com/blog/articles/159.aspx

Here is an idea on how you can incorporate your logo into the design: http://heathersolomon.com/blog/articles/166.aspx

For the Quick Launch bar edits you need to edit the ONET.XML file. In the XML folder of the site definition you are working with locate and open  the ONET.XML file. Within the NavBars element are child NavBar elements, the first being the top horizontal bar. The ones that follow are the Quick Launch items. Add/remove as need be and restart IIS for the changes to take effect.

As for the title changes, I would need more detail as to what you are trying to do. Some things you may be able to easily hide  using CSS.