To pollinate the same plant in order to get more of that plant's seeds, Self-Pollinate it. To do this, select a plant (white ring around the base of the plant's pot). Click and drag the pollen onto the SAME plant (white ring around the base of the plant's pot).

To pollinate a different plant in order to get a completely different seed, Cross-Pollinate it. To do this, select a plant (white ring around the base of the plant's pot). Click and drag the pollen onto a DIFFERENT plant (one that does *not* have the white ring).

I hope these two definitions assist you with your problems.