NOTE: These do not have to be fought in this order. This is just the order I fought them.

Boss #1:
Empress Bulblax.

Use any kind of Pikmin and throw them on her. Then, when she is about to shake, call your Pikmin and run to where you entered the floor. Repeat this until she explodes.

Boss #2:
Burrowing Snagret.
Separate your Pikmin and call the white Pikmin you found earlier. Take them to the Snagret and throw them at it's head. If it grabs some, it will get poisoned. It should be gone in a matter of seconds, but if it isn't, repeat this process.

Boss #3:
Emperor Bulblax.
Take white Pikmin and dismiss them in front of Bulblax. He will eat them. He should die almost instantaneously, but if he doesn't, throw either blue or purple Pikmin at his face.

Boss #4:
Beady Long Legs.
Use yellow Pikmin and throw them at the ball. Repeat. NOTE: DO NOT attack the feet. Attacking the feet is futile.

I've only gotten this far in the game, but I will be back, and I will call the title "Bosses (con'd)"