You can run External mode from a power-cycle boot. On your Simulink model, click on the "Code" menu option, then click on the External Mode Control Panel. Once your board is up and running, click on "Connect" on the External mode control panel, you can now tune parameters and log signals. The model has to be matching the code that is running on the target, otherwise you may get a checksum error. There is no provision to just save these parameters in flash right now, but the latest values you applied will be present in your Simulink model, even if the board resets. You just have to generate code again for the new parameters to be permanently flashed onto the processor, which is a one-click operation.
I hope it helps,