Iva,
Your method is good, easier, faster and less prone to errors rather than creating a new project from zero.
I would like to share with you a workaround I found in order not to mess with the original boards/frdmk64f folder files like gpio_pins.c, board.h, etc and get free to change them to meet my application needs. It may be helpful to other people in the Community.
1) I cloned (Ctl + C, Ctl + V) the "C:/Freescale/KSDK_1.1.0/board/frdmk64f" folder and renamed it, in my case, to "myboard_k64f" in the same directory, keeping the files inside with the same name:

2) Then, I created a virtual folder and named it "KSDK_Files" and included the linked files inside that folder. To do it, I right clicked on project's name, "New", "Folder". I filled the "Folder name" field with "KSDK_Files", clicked on "Advanced", checked on the option "Folder is not located in the file system (Virtual Folder)" and clicked on "Finish":


3) Right click on "KSDK_Files" folder. Select New / File / Advanced and mark the option "Link to File in File System". Click on "Browse" button and point to "board.h" file inside recently created "myboard_k64f" folder and click on "Open" to confirm:

4) Repeat the same procedure above in order to link to the other files: "gpio_pins.c", "gpio_pins.h", "hardware_init.c", "pin_mux.c" and "pin_mux.h". Do not link to "frdmk64f.peb" file. We won't use it in our case.
5) Now it is necessary to change the path which points to "frdmk64f" folder to "myboard_k64f" folder in "Compiler / Includes" and "Assembler / Includes" Settings:
5.1) First, go to "Project / Settings / Cross ARM GNU Assembler / Includes". Double click on the "...boards/frdmk64f" folder path and change it to "...boards/myboard_k64f". Click on "OK" and "Apply":

Repeat the same procedure above in "Project / Settings / Cross ARM C Compiler / Includes", rebuild the project and it is finished. Now you have you own board configuration files to do change acording to your board setup, without messing with the original ones.
Best regards,
Marco Coelho