It should be easier to go the Simulink path. The challenge you will have it is interfacing it with a Simscape Network. You will likely implement each cell as a voltage controlled current source. So the model will take a current as an input, and output it's voltage for the next time step. You can also have other inputs and outputs such as thermal data. This will be easiest if you can model at least some of the terminal resistance in Simscape instead of your P2D/DFN network but I'm not sure if you'll have that information. You can use a variable resistor so that it changes over time. There is also the issue of how to call the electrochemcial model from Simulink. One way is to use a matlab function in Simulink to call your model. If your model happens to be in c/c++, an FMI/FMU implementation, or have an s function implementation, you could also put it directly into Simulink.
Hopefully that gives you a little bit of an idea on how to start. Please feel free to add follow up questions as you try and move forward.
If you need some free training on the Simulink and Simscape models, please use this:
