Regarding the issue I was having about not being able to connect to the adobe system tables using mySQL, I found out the following:
The id and password and port are stored in the adobe-ds.xml file within the c:\Adobe\LiveCycle8.2\jboss\server\all\deploy directory.
Using mySQL administrator, on the initial prompt click the elipses next to the "Stored Connection" field and create a new connection using the port, id, and password specified in the file above.
I then received the message "either the server service or the configuration file could not be found. startup variables and service section are therefore disabled", which is addressed in this post:
http://michael.omnicypher.com/2008/11/mysql-configuration-with-adobe.html