Well, the guidebook doesn't say much that's actually helpful.

What I would do is leave your Pikmin with one of your pilots in a safe area, and bring the
Gatling Groink close to the Woolywogs. Start punching the Wollywogs, avoiding their
attacks, and the Gatling Groink should shoot at you, and if you're close enough to the
Wollywogs, and have good enough reflexes, the Wollywogs should get shot while you get
away.After that, all I can recommend is a Super-Bitter Spray on the Groink, or a bunch of
blues and good reflexes again. Make sure you bring the Groink back to the ship thing
before it revives itself.

PREES DOWN TO ISUE YOUR PIKMIN COMANDS IF NEAR WATER DISPAND SQUAD THEN PROTECT OTHERS
WITH WATER PIKMIN THEN ATTACK