Oh man this could get long and windy...
First, you are right about using one out for live, most of the time that is the case, and you are shure there are no phase issues.
Now I have many setups, for all kinds of situations.
For recording i have some really wild stereo sounds, that unfortunately can't be sent out to stereo amps simultaneously, because of limitations on the Helix so far,
so I have to have too many presets to make sure that I can cover the same sounds in different scenarios.
Please explain how you use the Libra inside the Helix floor, I don't get it.
Sometimes I have 2 parallel cabs (turned into mono via a simple eq.) and the feed stereo efx after that, but other times I have 2 different cabs at the end, and the have the spread/panning per preset.
I like to record that way too. On most presets I have a 10ms. delay on the right side for a spread. Then if I need a Mono-out signal, I have the left side "dry" so i don't need to switch the delay off (Helix Dual delay).
Did this help?