Here is what I am doing with my hunters. Anything I need to toggle I put on the visible pet bar. Cower/Growl/ etc. The talented abilities I leave them in the spell book, turn off auto cast and macro them. You can then drop the macro on an action bar and drag it next to your pet bar if you wish.

Pet abilities that are in your spellbook that have auto cast turned on will still autocast as expected. So there is no need to have your entire pet spellbook on the pet bar.

I hope this answered your question.