Hi Ugur:
Please refer to demo
Freescale_MQX_4_2\demo\pe_demo\build\cw10gcc\pe_demo_twrk60f120m
Please also refer to the chapter 3 of below document
Freescale_MQX_4_2\doc\tools\cw\MQX_Howto_Setup_Kinetis_Clock_UsingPE
Though this demo and docs are for Codewarrior, KDS is very similar.
Unfortunately currently no document for KDS
Regards
Daniel