How to add files to an MX generated project
You can add user folders and files to Eclipse project. It is nothing to do with ac6. To add folder or file, right click project and select folder or file. The easiest way is to copy folder/files from somewhere and and pase to project. ac6 will auto generate make file inside added folder. Do not forget to add user include path to project by right clicking project, and then popup Properties Configuration Window, Select C/C++ General, Path and Symbols, Includes Tab.
ac6 make file lacks dependency, so you may add -MT"$@" into Properties/C/C++ Build/Settings/Tool Settings/MCU GCC Compiler/Miscellaneou/Other flags.
I suggest not use ac6 auto generated make files, write your own make file to do what you want. Also it seems the STM32CubeMX directory structure is not so good to fit EClipse CDT.