Defining Parts
Define the parts as bodies in the PartDesign Workbench.
It is convenient to collect similar parts into a single file, because the files and the Parts therein are listed in the insert component dialog of the assembly workbench. Having one part per file would create a lot of redundancy and heavy need for scrolling in that dialog.
The placement of the parts in the file is irrelevant for the use in assemblies.
Give the parts a meaningful name (label property).
The color of part instances can be modified using a custom dialog. This also can be used to create consistent colors of the parts.
In order to avoid accidental modification from interactions in assemblies, set Display Mode Body (Base property of a PartDesign part) to Tip when the part is ready. For editing, set it to Through.