Hi Izzie,
Some advice already given but I think we need to look at the fundamentals first in order to be most helpful for you.
Firstly, I will make the assumption that you are using the tripod in your studio, if not you are wasting your time
You need to understand that the DoF is going to be 'limited' and you are not going to be able to get the entire depth of the flower in focus. Knowing this you need to decide what aperture is going to give you the the 'best' you can get (lets ignore diffraction for now) and I would suggest you start with f/18. (This can be further discussed if we know what lens you are using).
You now need to appreciate that the depth of 'best' focus is going to be 1/2 in front and 1/2 behind the surface part of the flower you focus your lens on.
Knowing the above you now need to look at your flower and decide what you want to be most in focus
You say that you 'tried' to put the focus on the white-ish bump in the middle but do not say how. It is extremely unlikely that you would be able to use 'auto focus' on this shot because anywhere you place the 'focus point' box within it there will be both near and farther edges/surfaces, it will be confused and you will not know exactly what it has chosen to focus the lens on. For this reason you should use manual focus and adjust to get the the part you want sharpest. If your eyesight is reasonable there is absolutely no need to use Live view in my opinion.
Until such time as you are fully confident at getting focus exactly where you want it in these 'studio' conditions you should not be worrying about lighting and certainly not considering stacking.
So, to simplify, practice getting your focus as you want it and also seeing the affect of using apertures between lets say f/8 to f/25 until you are fully confident.
Once that is mastered, lighting comes next.
Grahame