What you see also happens on my AMD Dualcore, but only after installing the dual-core optimizer from AMD. Otherwise (if I remember correct) without that one and the CPU driver a single-threaded app only runs on one core.
But with a specialized driver, the workload will get split between the CPUs, though I can't tell how that's exactly done. It also does that in most of the games that use only one core where they then only take up 50% CPU time on each of the cores. So I think it's a driver thing.
But actually this doesn't change any behaviour within the application itself, so except for correct timing you don't need to take care for multi cores.