When Bees are put in Apiaries and you have different kinds of trees around the apiary, the bees will randomly pollinate trees.
Do note that GenerikB is misleading you by saying that the bees pollinate based on where they fly.
The particles have absolutely nothing to do with it.
One of the best bees for Pollination is the Industrious Bee.
Breed up to the Industrious Bee, make yourself an Alveary and an Alveary Sieve, put a silk wisp in the Sieve (So you will need Tropical Bees), put different kinds of trees around the Alveary, and loop your Industrious.
This is best done in Normal, Damp climate as butterflies spawn easily.
I am well-informed in Bee and Tree Breeding, but not Butterfly breeding.
Yet.
Read up on Butterfly Breeding, because you will have a lot of them.