More than anything else you need to know about using MySQL with WebObjects, you must know to NEVER use MyISAM engine for tables.
For very complete notes about MySQL and WebObjects. See this [blog|http://homepage.mac.com/kelleherk/iblog/C711669388/index.html]. \[stale link\. [stale link] Wiki Markup
If you're interested in a nice graphical interface to managing your MySQL, you may want to checkout out Navicat MySQL from Navicat.