In case you want to program an existing application generated with Model Based Design Toolbox or any other IDE (e.g. the examples from the Motor Control Course) there is an easy way called RAppID Bootloader Tool.
Let us consider the following example shown in Lecture #12 - Motor Control System. This lecture contains a zip file Lecture #12.zip that comes with a pre-compiled FLASH application that you can find inside the ClosedLoop_Control_mbd_rtw folder: ClosedLoop_Control_mbd_rtw\ClosedLoop_Control.mot
Question: How to flash the *.mot file into the MPC5744P DevKit?
Answer: Use RAppID_BL.exe application via Serial Port.
Prerequisites: This tutorial assumes you have already programmed the RBF file into the flash memory of the MCP5744P microprocessor. The RBF is the target microcontroller specific algorithm, which the GUI interfaces to for
boot loader operation. Check Motor Control Class: ADC PROGRAMMING starting at 2.04 to see how you can program the RBF.
Step 1: Configure the MPC5744P DevKit board to use power from USB through the OpenSDA interface by setting the J13 jumper in the 2-3 position
Step 2: Connect the Board with the Host PC via the Micro-USB connector
Step 3: Check your computer Device Manager to see if the Serial Driver was installed and configured correctly and note down the UART port assigned (e.g. COM5)
Step 4: Navigate to the C:\MBDToolbox\mbdtbx_MPC574xP\tools\BootLoader folder and run the RAppID_BL.exe application
Step 5: Configure: Communication Protocol, Communication Port and select the MCU part you want to program.
Step 6: Load the *.mot file you need to program by clicking on the Browse button
Step 7: Select Auto Read File option
Step 8: Reset the board by pressing the SW3
Step 9: Very quickly (within 5 seconds from pressing SW3) press the Start Boot Loader button
Step 10: Wait patiently until the Erase&Program operation is finalized. The RAppID_BL.exe should show: Complete
Now your application is programmed into the MCU flash/ram memory. At this point you may change back the J13 to position 1-2 for external power supply.