Your post is a little difficult to follow, but you did a good job trying to explain. Based on what I think I'm reading, I will try and help you out. For starters, the WXHB is a lot easier to use if you just set it up to double tap L2 or R2 respectively. Whatever hotbar you assign to those functions, slot the skills that you wish to remain on screen most of the time.

The expanded controls by holding L2/R2 aren't meant to take the place of skills mapped to the WXHB. I will get to that in the next paragraph. The hotbar assigned to this function should remain hidden when not in use, which it sounds like it is. However, using this function should be replacing your primary hotbar on your HUD rather than skills on your WXHB because you can't use both at once.

Again, without being 100% sure clear on your post, I can't be sure but there are a couple of things you can look at. The game is set by default to cycle hotbar 1 and 8 by pressing R1 unless you have skills assigned to other hotbars, in which case it will cycle through all of them. The game has settings to change this, but if for some reason you are hitting R1 and you have expanded controls assigned to hotbars that are set to cycle, it will automatically change what you see on screen when that hotbar cycles to primary. Make sure you don't have the same hotbar assigned to multiple expanded control options. I have never tried this but I assume the UI will automatically pick one or the other on it's own.

I can't be sure this will help but I hope it does.