Hi, I feel your pain!
I spent a few weeks trying to figure out how to do the headstock and heel transitions. And even now I still have more work to do in order for the curves to be good enough to just do some finish sanding. If you search YouTube, you'll find numerous videos on the different ways that people have done these neck transitions. Some have used the Sculpt mode.......I gave that a try, but it seemed overly complicated. The method I finally used was the Loft function in Model mode. Loft will allow you to quickly generate transition curves that connect one profile to another profile. For example, between a rectangular profile to a circular profile. However, Loft tends to make straight lines between the two profiles, and the transitions at the headstock and heel of the neck are usually gentle curves. There is an option in Loft that allows the use of 'rails'. Think of a rail as a guideline that shapes the loft lines in the curved way that you want. I found that there's more tweaking needed in getting Loft to work well on these transitions, but I don't think I can easily summarize them in this post. There is a "Fusion 360 Luthiers" group on FaceBook, you could ping me there if you need more details about getting Loft to work.
Dan