Performance evaluation is an important step for designing embedded applications that require small footprints, low energy consumption and high throughput. We present a simulation-based method to characterize several resource properties (memory accesses, energy consumption, execution time) of embedded software that runs on dedicated processing engines targeted for SoC designs. The results of the characterization process are back-annotated to the source code to aid the designer in optimizing the implementation. Our approach allows the replacement of software parts by hardware units to speed up processing. We have performed case studies with software and hardware implementations of a pseudo-random number generator and a transmission error detector. The results show that computation speed-ups and energy reductions up to a factor of 15 can be obtained with implementations that exploit hardware extensions.