You can customise the button order. I'm presuming you're in Device mode for the amp? If your amp is anything like mine, the database will be clogged with useless non functioning buttons etc. so have a good weed out. They are listed in alphabetical order by default so rearrange them into the order you want. I have added my most commonly used AV Receiver functions to some of my activities.
I must admit though, after the Pronto, I'm glad I went for the Harmony One as I don't like the tablet/two handed approach and prefer hard buttons for the majority of functions. It's the best remote I've owned. Obviously you can spend a lot more going for the more customisable options from Nevo or Pronto etc. but I'm happy with Harmony.