Hi @philip20200426,
I am not following your question. Do you need to compile the project through S32DS IDE? The command line method does require S32DS to be closed, but you can generate the config tools code separately, build the project, and open the source code with external text editors.
There is also a section in the "Help" menu titled "Command Line Interface" for different commands within S32DS:

Please clarify your end goal using commands without visual indications.
Also, the compilation tool is GCC, you can find the build command and C compiler inside "Project Settings":

Best regards,
Julián