You can program any 28379D MCU directly from PLECS. For programming either the LaunchPad or the ControlCARD, select the appropriate "Board" type. For a custom board, choose "Custom", then link the downloaded .ccxml file from Uniflash, as mentioned in the TI C2000 User Manual (Quickstart > Program the MCU from PLECS).
I attached a simple example which blinks an LED (GPIO34) and generates PWM signals on GPIOs 0 and 1 of a 28379D controlCARD. Note that you can only program one of the cores of this controlCARD directly from PLECS. If you want to program both cores, you can generate code to CCS from PLECS, and then program from there.
For any other specific questions, please feel free to email email@example.com.