For now, I'd just use the minimal shoes for the odd shorter run and the cushioned ones for longer runs. Once you feel comfortable with that, start to increase the mileage in the minimal shoes gradually, Eventually, you should feel comfortable doing all your running in them.
If you continue with really bad pain whenever you wear the minimal shoes, it might be worth getting your gait analysed as their might be something not quite right there.
Ideally, once your running style has changed as a result of wearing barefoot, you would continue with that even in a cushioned trainer. There's nothing to stop you running with good form in a cushioned shoe, but the thinner soles on a minimal one almost force you to do it by making it uncomfortable to heel strike. Running in a cushioned shoe shouldn't automatically make you revert to your old way of running, but if you went back to them permanently, you might start to slip back into old ways.