Seperate your yellow pikmin from the rest of the group. Have one of babysit the rest while you take the yellow pikmin in to the pit with the boss. Next, use those pikmin to attack the electric pump. You can survive the other attacks by movement, but electricity will own your other pikmin--so get that pump out of the way by throwing yellows on to it. When you see the dweevil change color, react accroding. Red and purple means that you need to get of the pit. With blue, I find it works to take cover under the monster with you small group while switching back and forth between the groups to call pikmin who have been hit by water.
After some time attacking the electric pump (you know you're doing damage when you start seeing smoke), the pump will fall of. Go for the the water pump next since that attack cover the whole play area and not just the pit. If you use blue pikmin here, you don't have to dodge in the pit. You only have to worry about the water damage to pikmin outside. Attack and dodge similarily to the last example until you knock that pump out. Now you are left with fire and poison. It doesn't matter which order you use or what pikmin you decided to use because they won't die immediately and the attacks are easier to dodge. But stick with a small group anyway so you don't end up losing half you forces by not being able to wistle for all of them. Eventually the pumps will drop and you are left with the naked titan dweevil. He can't attack now so bring all your forces in and destroy him quickly.