For the most part I tend to use a variety of different techniques.
I generally have some sort of layout sketch, such as a general plant arrangement layout, a conveyor layout, etc. I will put this into a part file so I have more leeway as to hiding, suppressing, moving, etc in the assy, and mate it into the assy with something major at the origin. Depending on what the job is, this may be a column line, or it could be the center of a transfer - a work point - just depends. I may have a car body outline part that has three sketches in it - front, side, top, again mated in whatever fashion is appropriate. Then I usually find that as my design progresses, I may add some sketches in the assy to help define the location of something, or give me some ref dims to watch as I work around something else. These are all the basis of whatever I am designing.
Then I start with something like the carrier that will handle the body. This will go into the assy in such a way as fits the scope of the job. Maybe I want to be able to move it along a path and see how it chords around the curves. I may have a fork transfer that moves the car from an inverted carrier to an overhead carrier, and that transfer is mated with its system planes to the assy, usually to part of the layout sketch. I might have some tooling that travels with the carrier, so it gets mated to the carrier in the assy.
So, as you probably already know, there isn't one right answer, and probably not always even just one that fits the job. Having many tools in the box, and enough experience to know how and when to use each one, generally leads to a better SW experience.
WT