Yeah, I trained myself when it came out to use it, and I beat a lot of the issues by having my most common alt-bar skills (Heavy Thrust and Leg Sweep) in the same place on both sides (Y and down, respectively) so I can use them regardless which one I open up.
And I know this isn't the thread for it, so under a cut:
You really shouldn't use the Pet Hotbar on any pet classes. The only skills you need off it are their main skills; the place/obey/etc can be relegated somewhere hidden, while Embrace/Whispering/Covenant/Illum/Wind should be on your main bars (I use tricky stuff that swaps those skills depending on which pet I summon).
And BLM is the easiest - so many of your skills become useless as you level up that you end up with an extremely small array of buttons that you actually *need* on your bar. There's so few that I even put Freeze on for maximum fun.