Have you tried using the documentation or using the Wiki? This question is too broad to be answered in a forum.
You will get more help with specific problems rather than very broad questions.
I would suggest that you start with the 'JBoss Eclipse IDE' link to the right of the page and follow the documentation to get JBoss and Eclipse together.
Deploying datasources is documented in numerous documents from the getting started guide to the administrators guide. For the moment I would recommend you don't touch the default datasource and just deploy a new datasource to use for your own persistence, once you understand JBoss better then you can switch to use MySQL for all persistence.
Is there a reason for the specific Tomcat version, JBoss 4.0.0 already has Tomcat 5 bundled.