I have been in the same situation like you last fall, and getting past the simple examples ain't easy. There was more than one occasion where I honestly considered going back to gadtools + costum BOOPSI-classes, but after I finally gathered some understanding, I would never go back.
O.k. some of my problems may have had something to do with the fact that I allready had >300k sources completly unprepaired for MUI .....
And as Tokai wrote, useing RETURN_IDs may look convinient, but is a pain in the end. So you will need atleast one costum class, where your apps "intellegence" is gathered. This may be based on MUIC_Area, when it represents a part of the window, or based on MUIC_Notify when it is just for receiving and sending commands.
If your program gets bigger, you might want to split of this into several classes.