Hi
I had the same problem as you are. With the macro lens - mine's 100mm - some of the flower would be out of focus, and it was really starting to annoy me. It wasn't until I was chatting to someone who suggested using my standard lens, in this case a Canon EF 17-40mm zoom to take the shot. What a difference, as it enabled me to take the same shot but with the whole bloom in focus, without losing any of the detail. It does mean though getting quite close, but that's no big deal. In these instances I do use a tripod, and a remote shutter - as I'm still trying not to wobble the camera
I've attached a shot I've done using this lens just to show you what I'm talking about.
I'm no expert, but i'm sure someone will explain in my case why this works!