How do I choose which plat is used to supply the pollen?

You select any plant you want and if the plant is mature it will have pollen available in the left handle panel. You can use that pollen on that plant, or drag to a different plant to cross pollinate.

And you can see which one is selected by the blue ring that appears around the base.

So if I click on a Venomous Grass, then drag the pollen to another Venomous Grass, I'll be breeding 2 Venomous Grasses together? What happens if I click on a Lemon Maranta, then drag the pollen to a Venomous Grass? Will they cross breed?

Yes, that's basically how it works. In your cross-pollination example, you'll get seeds for a different species of plant.

I've managed to get a magic plant, and yet I still haven't figured out how to breed properly. Doh!

Thanks guys!