66AK2G12: How to use output files generated by PINMUX tool and Clock tree tool?

Hi,

My customer used PINMUX tool and Clock tree tools and generated their own configuration files by these tools.
Their custom board will be ready for debug next month.

Question)
It is not clearly documented how to use these output files for code implementation and/or debug.
Are there any good document or examples?

Thanks and regards,
Koichiro Tashiro