The key to understanding the breeding is realizing that the flower types and the foliage types are independent. When you select plants for pollination, you have to consider the flowers and foliage separately.

You will get confused if you try to randomly breed and keep every kind of see you make. The seed trays aren't large enough for that.

The only seeds you absolutely need to keep are the common (Tier 1) seeds, which include the Reptans, Astera, Maranta, Maple, and Ball Cactus foliage types and the Spotted, Bluestar, Jalapa, Four-petal, and Ball flower types. All other Tier 1 through Tier 3 seeds (and the Magic Plants) can be created from them with one or two generations of cross-pollination. The Tier 4 plants can come later, when you have enough money for Exotic seeds and Mutation Liquid from the store.

Maybe you will find the breeding advice in this guide easier to follow.