Do you shoot RAW? I never mess with stuff like white balance until after...
I shoot both RAW and jpg. Mostly jpgs now though, cause I hate booting into Windows. Shooting auto-white balance in jpg's make a big difference. In RAW not so much, but it's definitely noticeable. The colors are just that much clearer right out of the glass, which leaves me time to post-process them for further refinement.
Use your aperture to control the DOF (depth of field), and with flowers/macro you can also use the manual flash settings to further the control.
I started with a fully manual film camera, and when you have to set the aperture/shutter speed/exposure comp/etc, you learn what these things do, and you learn to use them to your advantage... so maybe you could set the camera to manual for a bit and see how these things relate to each other?