The short answer is, ideally, that your code will remain the same, and all the hard work is done by Conitec.

The most common solution to multi-threaded games is to split things up into large groups (sounds, physics, graphics, AI) and put each of those in their own thread.

Using this method, all of your C-script functions would run on a single thread (AI). They will run just like they do now but, instead of getting 5-10% of the CPU time each frame they can have 100%.