kazanaki is right, the java files that are generated can be modified but the resulting .java files are notoriously messy, large and hard to interpret. Also, you cannot change some things (as noted in the comments in the generated .java file) without rendering matisse useless because it expects the file to have things in a certain way. That being said, if you are careful not to step on Matisse's toes you can code away and it will not touch your code which is nice.
Outlaw is right too, if you change anything that is already in Matisse's perview it will be overwritten. Any changes that you make outside of matisse must be outside of any element that is covered by the xml that matisse uses to generate the code.
I have tried this kind of thing before with limited success and eventually just rewrote the interface to avoid these maddening headaches.