During the Clone Wars (events on Episode II/III), I find it difficult to understand the relation between the Chancellor and the Jedi Council in terms of authority over the Clone army.
Technically, the clone army belongs to the Republic, which is ruled by the Chancellor. Since he's been granted emergency powers by the Senate, he should have the ultimate authority over the military decisions.
But the Masters in the Council are considered Generals, and on several ocasions we see them making decisions about military strategies, without consulting anyone else, as if they have this autonomy:
MACE WlNDU: Then the Jedi Council will make finding Grievous our highest priority.
OBI-WAN: In short, they are going very well. Saleucami has fallen, and Master Vos has moved his troops to Boz Pity.
YODA: Go, I will. Good relations with the Wookiees, I have.
MACE: It is settled then. Yoda will take a battalion of clones to reinforce the Wookiees on Kashyyyk. May the Force be with us all.
On another ocasion, Obi-Wan even called it Jedi Affairs:
OBI-WAN: The fact of the matter is you're too close to the Chancellor. The Council doesn't like it when he interferes in Jedi affairs.
And they get upset when the Chancellor tries to interfere in the decisions:
MACE: The Council will make up its own mind who is to go, not the Chancellor.
So, what is the military position of the Jedi Council in the Republic? How is it that the Clone Army belongs to the Republic and to the Chancellor, but the Jedi use them anyway they want?