Start planning your cooldown usage according to boss mechanics and such. Basic rule of thumb is to time haste cds with agi boosts whenever possible:
Morchok: Rapid fire at the start instead of midway through to line up with your call of the wild/pot/synapse and polearm proc.
Zonozz, Hagara: Save your rapid fire until the damage buff phases, and the latest one possible on Zonozz
Ultraxion: If you're using rapid fire near the start of the fight, use it immediately. The way you staggered it left it still on top of hero but after your pot and synapse springs ended. If you're going to stagger your rapid fire, save it until the end when you can start using kill shot, use your re-pot and ideally try to time it with your polearm proc and synapse springs.
Also, Kill Command shouldn't be used at all.