To make this faster and easier, get the yellow pikmin first. 
Then go to the "Impact Site" level and go into the part past
the box with the number 10 on it. Have the yellow pikmin pick up the
bomb rocks on the other side of the box, and use three of them to
knock down the white wall.  Once you go inside, stay close to the
sides as not to drown your pikmin. To the right, around the corner is
a clam type thing with a pearl in it's mouth. Stand next to it and put
your site in it's mouth just next to the pearl. Grab a pikmin with a
bomb rock and toss it it. It should land in, run out and throw it's
bomb rock. Do this twice to kill it. Have them take it back to the
onion and you get about 50 pikmin seeds!!!