Hi, and thanks for the response. Sorry for my late reply, I was out of town over the weekend.
To program individual buttons, i used the procedure in the manual, which was:
1) While holding down the mode button (TV, DVD, etc), push power for 3 seconds.
2) On, the Onkyo, push the button you want to learn a command
3) aim the 2 remotes at each other, and on the other remote, puch the button you want the Onkyo remote to learn
That's it. It was quite easy to set it up to learn all my other devices.
What I was thinking I might do, is use an unassigned mode to lears the commands from the Yamaha. Thta might get me some menus and the like, but i don't think full control over the device (input select, audio decoding switching, etc).