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Joined: Mar 2006
You shouldn't need to worry about the really thin, stringy roots. However, you shouldn't cut through any roots bigger in diameter than your thumb, and, especially for the shrubs, I think I'd try to avoid cutting through too many bigger in diameter than a pencil. Make certain that the tools you're using are clean, and be sure to mulch the area well afterwards. Trees and shrubs pull a lot of moisture from the ground, sometimes not leaving much for the flowers. Mulch will help to conserve whatever moisture remains, but you'll still want to check the area regularly and give it some extra water as your new flowers become established.
The great thing about gardening is that you always get a chance to start over!