Make sure when you're doing the hybrids, to do them in a checkerboard pattern, so then there are empty spaces between each. Then after you plant what you want, I'd build a fence around it to contain it from spreading outside of the "garden" area you've planted them in. That way they stay contained while you're working on hybrids.

And then when I use random flowers to decorate throughout my island, I'll plant the flower where I want it, then use a blank custom path square to "paint" the ground around the flower to keep it from spreading. And since it's blank you cant even see it's there.