Both my Olympus and Panasonic cameras have a focus bracketing feature that allows me to focus on the closest part of the flower with the first shot, followed automatically by sequentially further-focused shots. The beauty of this feature is that this is done with one press of the shutter and at a speed of approximately 10 frames per second.
May's images and post about photo stacking flowers mentioned I had assembled the May images using Zyrene Stacker. In June I instead used photoshop, and I prefer the results it gave me. And of course, for those who already subscribe to Photoshop and Lightroom, there is not the additional expense of buying a plug-in like Zyrene Stacker.
Basically, I find Photoshop does a better job aligning the flowers. As a result there is rarely any ghosting, something I more than occasionally found using Zyrene Stacker.
Generally, I shot 20 images at a time, starting by focusing on the closest point of the flower. In Lightroom I viewed each image and deleted any that were focusing further than the farthest point of the flower. In some cases all 20 images were useable. In one case, I only used the first seven images.
In all but two of these stacked images I shot wide open at F2.8 (60mm macro) and F4 (12-100 zoom).The two exceptions were at F4 on the macro lens.
With a couple of exceptions I sought hazy or cloudy days. Light of any kind is good, but diffused light is the best!