How to add files to an MX generated project
I still struggle with some of this myself but,
possibly I can offer some thoughts.
I have been twiddling with the STM32CubeMX and System Workbench, and I find that the STM32CubeMX structure is good for me.
It putes the BSP in the Application/User folder where one also finds main.
Most of the files listed in the project appear to be in virtual directories, that is, I see them in Eclipse in one way and if I look on the disk drive, they are in different places.
I found that you must use the import to bring in more .c files and also .h files, after some experiemnting with the import and multiple failed attmpts, I seem to be able to duplicate my efforts with some twiddling.
Once you get used to Eclipse, the rest should fall into place.