At 41m55s in this video, it is said that after the Russian Supreme Council voted to leave the USSR there was a period of dual authority. During this period when the Soviet Union wasn't completely dissolved and Russia was independent, who did the Soviet Army stationed on Russian land take their orders from?
I think you are aking for clarity in hindsight which did not exist at the time. Loyalties were shifting and individuals might not have known whose orders they would have followed if push came to shove.
Remember the August Coup. The reactionaries called up the military, the military deployed to Moscow, but then some tanks in key locations tanks went over to the other side. Yeltsin spoke on the tank. That tank crew let him, and others around did not prevent it.
Meanwhile, other troops were still planning to attack the parliament but ultimately didn't dare/want to do it.