The Engine is relatively easy to get. First spawn and grow all the Pikmin you can. First you grow the ones already around you, then use ten of them to push the box, and then grab the rest of the pellets. You should end up with approximately 25 Pikmin, and all you need to grab the engine are 20. So use them to do the job. Remember to use the Free Flower Pikmin technique.
Positron Generator (yellow and blue Pikmin required)
First use the yellow Pikmin to take out the stone wall, for the Positron Generator your going to need to take your blue Pikmin and head into the pond. Find the Clam that has the funny shaped piece in it. Throw your blue Pikmin on the clam, now watch the clam! As soon as its top starts shaking its going to slap shut, and will kill any Pikmin inside it, so just call them right before it does.
The more important part of this level however are all the other clams. They contain pearls, ans when your Pikmin bring the pearls back the same way they got the Positron Generator out, each pearl will yield 50 Pikmin. An amazing count. Also, there are 20 sized pellets around, one for each color Pikmin. It may take some practice before you can get it all in one go.