Hello ruihang.wu@magna.com,
Unfortunately, we do not support flashing the board directly from our toolbox over JTAG.
The toolbox comes with two ways of code deployment: one is the OpenSDA, which you are already familiar with and the other is using RappID bootloader, which requires flashing once over the JTAG from S32DS the bootloader and then the code will be deployed over Serial UART connection. This requires an USB to serial converter on the UART pins set in the Bootloader.
For the S32DS, the method you are using right now, if you are not debugging the code on the board, you don't have to import the generated code every time. You can use the Flash option, set a debug configuration project with the right settings for flashing the board, Disable auto build and select the generated elf that you want to flash. In the window below is how to flash the Bootloader but you can replace the .rbf file with the generated elf file.

Hope this helps,
Marius