I'd leave them both in there. Clock doesn't start ticking until the last bit of ich disappears from all fish in the tank.
Assuming you have some other type of biological filtration on the tank, I'd take out the sand. Using a bare bottom QT allows you to siphon the bottom off daily and keep a much cleaner tank. I'd read somewhere (and of course can't find it now) that the ich parasite will often drop off at night, ending up where the fish normally sleeps. It will then reproduce there - kinda sneaky since the fish will normally come back to the same spot to sleep. Once new generations of parasites come to life, the fish comes back to sleep, and gets a new crew of parasites.
The hypo will eventually kill all generations of ich, but if you can keep the bottom cleaned it may speed up the process.