the CGM is supposed to keep seeds from germinating, so I would think that if you put in seedlings instead of seeds, the flowers should be okay. But I am not real familiar with using CGM. I have read alot about it, but never used it myself. You may want to ask someone on the organic gardening forum. There are probably more people there familiar with CGM.

How old is your native plantings? And how big is your planting?

Usually as the native planting ages and becomes more mature, annuals are less likely to be successful. However I do know that Poa is very hard to get rid of and I have heard alot of people on these forums complain about it. So you are not alone.

On small plantings, like a small yard, I have found that hand removal of weeds is the most effective thing that you can do. Of course its simply not practicle on anything with a bit of size to it....

Good luck with your planting... it sounds lovely.

And we always appreciate pictures :-)