I would say, it depends on the type of the houses; modern, traditional, hunted, alien, spell caster, vampire, etc.
I'm not saying that my way is the best, but, what I did is,
1. I place the tree first
2. Then followed by the flowers/bushes that I want, either around the house or just below the windows, or even along the pathway. Play with the height & colours.
3. You can also add in the little wildflowers under your trees to make it looks nicer
4. Then use the terrain paint under the trees, bushes, & the flowers.