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KitProg found on the CY8CKIT-059 kit cannot be upgraded to KitProg3 due to hardware limitations. The hardware design is unchanged between KitProg2 and KitProg3. As a result, any kit that supports KitProg2 can be upgraded to KitProg3.
As I see that mode can be changed via the Programmer, so no need of switch and have to direct the additional IO's to the other headers.
You can only change between the modes on KitProg by holding down the reset button of the kit for more than five seconds. There is no way to do this via any tool. Please refer to the KitProg User Guide for more information on this. However, with KitProg3, the mode switch is available to switch between the modes and also comes with a Firmware Loader CLI tool that you can use to switch between the modes. Since your kit does not support KitProg2, it is not listed as supported in the KitProg3 User Guide.