How to implement a control system
Since you are implementing this system in a micro-controller, you would be better off converting your design from continuous time to discrete time.  You are going to  need analog to digital converters for you're inputs and digital to analog converters for your outputs.  The math should be simple to implement.  You're code will be based around a regular loop that samples inputs and updates outputs, not necessarily at the same rate as the system sampling rate.  You should make the timing through your control loop something that can be controlled with a parameter of some sort.  The dynamics of a discrete time control system are greatly affected by loop timing and delay.

I would recommend the following book: http://jeffreystevens25.blog.com/2012/10/26/online-applied-control-theory-for-embedded-systems/ 

Have fun!