Hello @PrabhuNex,
By default, the generated code for the S32K116 uses the external clock, settings made for the EVB board. If you want to change those settings, each time the code is generated, the s32k_clock_init.c file is copied from the {Toolbox installation path}\mbdtbx_s32k11x\src\c_library. So you can change the settings in that file to use the Internal fast clock. The C structure from the file is generated using the S32DS so you might find this information useful.
Regarding the BQ769x2 IC support, unfortunately, we do not provide support for that so if you want to include and use the custom code please have a look at this article https://community.nxp.com/t5/NXP-Model-Based-Design-Tools/How-to-use-your-own-C-code-in-our-Toolbox-... Also, in our toolbox you will find support for the MC3377xB Battery cell controller family so you might consider the usage of this MCU as well.
Hope this helps,
Marius