I grow about 90 roses in my yard, plus a variety of annuals, perennials and flowering shrubs, most of which are in formal beds. I have not had any problems with my dogs getting into the beds, but I will tell you that it takes a lot of extra time and effort to make sure they understand that the beds are off limits. My dogs are rarely outside for more than a few minutes unsupervised though. Most people would find it far easier to just move the plants to the front yard or fence them off.
I totally agree with lblax in that you should not allow them to accompany you when you are doing gardening chores, as this seems to encourage them to "help" you.
It takes a lot of patience and persistence, but I have not had one of them dig in the beds or chew one of the plants up. Then again, roses tend to teach their own little "lessons"
to those that mess with them, so they usually learn pretty quickly to leave mom's roses alone.
Please make sure that the plants in your flower garden are non-toxic to pets. There are a number of popular flowers and bulbs that are toxic to dogs (i.e. daffodils, hyacinth, foxglove, iris, peace lily, azaleas and rhododendrons, lily of the valley, english ivy, oleander, hydrangeas) as well as cocoa bean mulch, and most pesiticides and fertilizers. Organic does not by any means mean non-toxic. For fertilizer I use only composted manure, fish fertilizer and alfalfa tea, and only when absolutely necessary, low toxicity chemicals to control disease and insects.
Check out the
ASPCA website for a list of toxic plants and good luck with your little one.