Yes and no... The caster has complete control over them in that only he can order them to do anything.
Skeletons and zombies only understand very simple commands, though, and have no initiative. Similar to golems in that respect.
So the caster's will tells them what to do any nobody else can. But the caster is not controlling their every action, and is not aware of them and what they are doing at all times.
The souls, as far as I know, are removed from the afterlife to sit helpless in the bodies.
Note more powerful undead (ghouls, wights and onwards) are sentient and free-willed, but you don't get them with the BG2 spell. In pnp, these are created by other spells such as the aptly-named
Create Greater Undead.