The only way to learn synthesis (or any other technical matter) is to read the manual while mucking around with the interface.
A modulation matrix is simply a way to assign a controller to a target. The simplist is the pitch wheel on most keyboards - it is usually hard wired to the oscillator pitch. But a matrix lets you do more complex things - like an lfo to a pitch, or envelope to the amp - all standard things and in most softsynths available from a drop down menu on the target.
Z3TA's matrix let's you interpose other controllers inbetween the first one and the target, much like a modular analog. If you read the manual it will take you step by step of what you can do. Patch those up and get a feel of how it works. You can do simple things like have the filter freq track the keyboard pitch (a standard"trick'), reverse that process, make it wider or smaller. Basically, you start with the controller, see the target and then change how the interoperators affect the process. It is easy to get lost if you don't remember the first slot and the last.
@