Do you know anything about diving independents or are we just jumping in here with both feet???
The empty bottle???? There is no empty bottle for a number of reasons. You switch you regs every 10, bar, 20, 50 bar whatever, so you drain both bottles at the same rate. You leave enoughg in each bottle to do you deco stops and away you go. The main reason for this is so yo don't end up in the exact situation you mentioned.
I'm using idependents to do dives i could do on a single cylinder, i.e. minimum deco. I use the second cylinder for redundancy not increase the available air.
You seem to have this obsession with training. I'm not a cave dive, i don't penertrate deep wrecks and i tend to dive a single cylinder. However i would like a bit of redundancy on cetain dives without the cost of fixed twins. A pony would be nice but essentially works out at the same cost as a second bottle so i went with a second bottle. Not the ideal set up but better than a single cylinder.