What I'm saying is that a university textbook will be written to be as general as possible within a certain subject. When I took mechatronics, I specifically used the PIC32 microcontroller series, but the textbook I had for the class only generally covered what microcontrollers can do (interrupts, timers, etc.). The rest I had to learn from the datasheet and from other documentation from Microchip. The link I included above is the textbook I had. A quick Internet search will point you to more specific materials on AVRs and what others have learned about using them in projects. I would think that's enough to get you started.
Depending on your interest level, you might not need to learn everything about mechatronics to get your specific idea/project underway. Don't make the mistake in thinking you have to know *everything* about the subject to start playing around with the components. Of course, that's not to say that there isn't a lot to learn, but don't think you have to take a university course to do something cool.