Hi Nicolas,
probably it is more easy when you start with the provided template project within the Build Environment and try to integrate the additional hardware components where you have generated the intialization code by CubeMX. This means, based on a running UI application you can start integrating the SPI, then the next hardware component...
The other way - integrating the entire Embedded Wizard code into a CubeMX generated project - is more challenging...
By the way: In the near future, the combination of Embedded Wizard GUI and CubeMX Initalization code will be more easy - but at the momement there is some manual integration work necessary.
Best regards,
Manfred.