The layout of the portal is defined by *-object.xml file. Do a search for files by that name under jboss-portal.sar, you will find several of them. The primary one is in conf/data.
To change the logo, though, you need to modify the theme. The themes are found under jboss-portal.sar/portal-core.war/themes.
I am giving a presentation on this topic (customizing the portal) next week at JBossWorld. At some point, my presentation should be available on the JBossWorld web site. That presentation gives more details.
I didn't really want to change the themes, rather, I wanted to take out things like current user, registration, greetings, the info in the middle ... I just want to make a simple intranet portal that every will have access to.
Do I just download the jboss-portal.sar source and remove that stuff?
The simple answer is "yes." All of those things are defined in *-object.xml files.
By the way, you said you read tutorials, did you read the JBoss Portal documentation? They explain how the portal is laid out using *-object.xml files.
Also, if you do not change the theme, the header will still declare that the portal is the "JBoss Portal". To change that, you have to change the logo image in the theme.