After you blow up walls with your Yellow Pikmin and have bombs remaining, keep them. They are very useful for defeating enemies. Keep the Yellow Pikmin with the bombs away from the group though because if a bomb explodes, your entire group will die. To use the Yellow Pikmin with a bombs, throw them at the target and call them back. Bombs will either seriously injure or kill the enemy. If the enemy is not dead just call your Pikmin to finish it off.