I used all parts using the imx6sxsabred Board Kit. Now I want to run it on my own custom board The other part is the pin setting part. I want to know which parts of the existing build file should be modified and how. Please explain in detail.
My suggestion is to use the Pins Tool for i.MX in order to configure processor's electrical properties related to all its respective pin signals; this tool generates a pin initilization code and a .dts file that may serve as reference for creating your device tree an pin mux configuration.
From your previous comment, I assume that your board is already developed, so you may want to review the I.MX Porting Guide