hardware changes & kernel rebuilds

How exactly is this catered for? In the source tree include/nios2_system.h is a file in my kernel_1c20 directory created when I generated the kernel project.

If I change and rebuild my system (sopc builder), i.e add new hardware, move something in memory etc, how exactly do I "reflect" these changes to the source tree so I can rebuild the kernel to match the new hardware configuration? I can't find anything about this in the documentation.

Thanks.