Are you using ArduPilotMega or ArduPilot. If you are using ArduPilotMega you can use the mavlink protocol and the mavsim toolbox that I have already developed for Scicoslab. This would make sending the data very simple. If you want to develop the block yourself you would just need to modify my existing mavsimHil blocks to do this. If you want me to do it let me know and I'll try to make a block by next week.
If you are using ArduPilot then you will need to develop the C++ code to send the old protocol messages. You can use the boost asio code already in the mavsim library to do this. See the existing mavsimHilBlocks again.
To use the existing hardware in the loop setup simply code the controller on the micro-controller. You can test the controller without the hardware by creating a model of the same controller in Scicoslab. See the wiki.