I believe you are planning to use the backup domain (i.e. not power PSoC 6 but run RTC from VBACKUP). If that's the case, then you need to set the switch SW7 to SuperCap position. But before you that please ensure your super cap has sufficient charge. You can use the Cy_SysPm_BackupSuperCapCharge API to enable the charging of super cap while VDDD is present. Note that this charging is slow and can take hours to fully charge a super cap from 0 V.
If you plan on using the VBACKUP to only keep RTC running even when the board is not powered, then all you need to make sure is your super cap has sufficient charge.
Once you have the switch in the super cap position and super cap has sufficient charge, you can disable the PMIC that controls the VDD supply of PSoC 6 while the rest of the kit is powered or you can simply plug-out the power to the board. The RTC should run as long as super cap has charge above 1.4 V. You can use SW2 to enable the PMIC again if the kit is powered.
You can refer to the PDL documentation about Managing PMIC and Back up domain under the SysPm Driver here (default location): file:///C:/Program%20Files%20(x86)/Cypress/PDL/3.0.1/doc/pdl_api_reference_manual/html/group__group__syspm.html.
Also refer to FAQ#29 for a known limitation on using P0.4 for PMIC wake up in the Kit user guide.
You can refer to the backup domain chapter in the TRM as well to understand the architecture better.
Let me know if you have any specific question in mind.
Meenakshi Sundaram R