Very simply:
As long as the spirit is in the binding enchantment and you are in physical contact with the binding, you can give him orders. He can not perceive the outside world without magic, but can use his powers, including casting spell. For me, he simply needs to cast a spell like second sight to perceive the outside world, and he can cast his other spells either on somebody in contact with the binding or on target perceived through second sight. Of course, spells are not automatically usable or useful (casting repair on the wearer of a matrix is not a very efficient use of MP). But no need of spell to give orders.
On the other hand, if you release the spirit from his binding, you can give only 1 order, but all the limitations on targeting or use of powers/spells are lifted. A control spell, whether spirit, runic or sorcerous, is required to be able to give several orders (including a last one to go back to the binding), including changing targets. I have not checked in RQ2, but it is exactly the same rule as in RQIII.