The detailed answer would read like a book but in a nutshell, do as much modeling as necessary to capture the design intent of the new product as a single, multi-bodied part file.
The object is to capture the crude size and shape of the parts and the interfaces between the parts of the product, e.g. common mounting points, the product envelope, key locations that multiple items in the product need to reference, keep-out zones and the like.
Then, "insert part" this top level base model as the first "feature" in all the part files of the new product, "delete body" on the pieces that each particular part isn't concerned about, and begin refining/detailing the individual parts from there.
Instantly you'll be light years ahead of the way 99% of the rest of the world does it, and the first time you have to go back to the top level base model to change the location of the primary mounting hole, and each and every part in the design that references that hole updates automatically while you were blinking, you'll understand why.
All the holes will always line up, and building assemblies becomes a "drag and drop" exercise since everything is modeled from the beginning in its correct location "in space" relative to everything else.
This also allows for easy coordination and modularization of the design effort because you can give chunks of the overall design to different teams who base their development work off the same "over-arching" base model.
This is often called "top down design" by uber cad nerds by the way.