I modified stage 9 boss because using both the meteors and the charged spikeball is a waste of ammo.
Assuming I didn't miss any ammo limitation, here is a possible ammo usage for the other 2 bosses :
Boss n°2 :
Charged Missile (49/10)
Charged Star (43/9)
Charged Missile (39/8)
Meteors (29/7) (19/6)
Whirlwind (15/5) (11/4)
Whirlwind (7/3) (3/2)
Charged buster (1/1)
Charged buster (0/0)
Boss n°3 :
Charged Spikeball (47/10) (39/9)
Charged Spikeball (31/8) (23/7)
Whirlwind (19/6) (15/5)
Whirlwind (11/4) (7/3)
Charged buster (5/2)
Charged buster (3/1)
Flame/Star (0/0)
After this there should be 1 uncharged Dirt for s11, 10 Bubble for the skips/damage and 1 unused uncharged Spikeball (now that I think about it, we can use it at the end of s9 boss instead of the charged Flame), though some attacks can be replaced by a Flame or Laser if needed.