Hello Kate,
if you mean the flash programmer which was part of Code Warrior for example, it will not be implemented in S32 Design Studio.
If you want to load 2 different elf files, please use debug configuration.
First, click on the lightning icon

Create new PeMicro Interface Debugging configuration. Choose 2 elf files and click Generate ELF Fields.

Specify paths to elf files.
Last, check all other debug settings.
If you have any other questions, please feel free to write me back.
Regards,
Martin