I'm not sure which questions still need answered but i'll go into some depth with screenshots. One quick note, the materials are not downloadable from 'Physical Materials' because they are pre-loaded in Fusion.
For Materials:
One a material is added to the design it can be modified. Those materials in the library that are provided by us are not editable in the materials manager within their folders and locations. However you can add any material to favorites and edit them there:

Once added to favorites you can rename and modify anything you'd like:

Lastly you can create a new material at the bottom left corner:

I would advise that these are placed in a different directory or a new directory to keep them separate from the provided materials.
For Appearances:
The same applies for materials manager, you can add to favorites and modify:

And the option to download an appearance should be here from the appearances dialog:

Again, once added to a design it should be editable.
The best option for editing either one is to add to favorites then make modifications. Additionally for appearances you can add to 'my appearances' to have them upload to the cloud.
Ryan Bales
Fusion 360 Product Support