Hello, @Sam_ECU
The NXP`s Model-Based Design Toolbox for IMXRT Platform has been designed to support different MCU hardware parts from IMXRT family. So, the toolbox is oriented to MCU chip itself, not to a specific hardware board. In this way, we are letting the customers to create their own custom hardware designs. Only the examples delivered in the toolbox are testing using the evaluation kits delivered by NXP.
Unfortunately, the IMXRT 1062 part that you are using (MIMXRT1062DVJ6B) is not supported in the latest release of MBDT for IMXRT Platform (see the attached image from Release Notes). But since I did not notice any major difference between MIMXRT1062DVJ6A and MIMXRT1062DVJ6B, you could try to select the MIMXRT1062DVJ6A hardware part from your Simulink model hardware parameters and build it. We cannot guarantee that the generated axf file will work, hence the specifications from Release Notes.

Basically, the generated axf file can be deployed using MCUXpresso. If your custom board has an OpenSDA, you can deploy automatically the axf file from Simulink, choosing the OpenSDA download method from the Hardware settings of your model.
Hope this helps you!
Let me know if you could manage to deploy the axf file generated from Simulink to your custom board!
Best regards,
Stefan.