Having gone through the transition from Inventor to Fusion myself, I totally understand where you are coming from.
Regarding parts/projects and folders--make sure you think it through and get it right the first time. Re-creating projects and moving files within them can be a pain and time consuming. What we have done is to create one project for our whole company. Within this project, we have various folders for purchased/sourced components as well as a number of folders for projects we are working on. As long as all of the files you are using are within the same project, they will keep their associativity (shown by the chain link icon). When I started using Fusion, I created a different project for each project I was working on as well as for each type of sourced part (fasteners, heat exchangers, etc). Makes sense, right? The issue is that associativity is not kept between projects. This can be a real issue if you made a mistake or the sourced part is updated, as the changes would not be reflected in the instances you used the part in.
If the part that I am creating may be used in other assemblies or designs, I create it within its own file and insert it into the assembly. If it is specific to that design, I create it within the assembly.
Fusion has a similar update feature to Inventor called "Get All Latest". It is an exclamation mark/chain link icon that appears around the upper left corner of the window.

Clicking this should update all linked parts. I say "should" because if you have inserted an assembly within an assembly, you may have to go back to the inserted assembly and update it before the larger assembly can be updated. The Fusion team has plans to implement a "deep update", which would do this step for you, but this feature is not yet in place.
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