As the complexity of embedded systems grows, design space exploration at a system level plays a more important role than before. In the system-level design, system designers start from describing functionalities of the system as processes and channels, and then decide mapping of them to various Processing Elements (PEs) including processors and dedicated hardware modules. A mapping decision is evaluated by simulation or FPGA-based prototyping. Designers iterate mapping and evaluation until all design requirements are met. We have developed two profilers, a process profiler and a memory profiler, for FPGA-based performance analysis of design candidates. The process profiler records a trace of process activations, while the memory profiler records a trace of channel accesses. According to mapping of processes to PEs, the profilers are automatically configured and instrumented into FPGA-based system prototypes by a system-level design tool that we have developed. Designers therefore need to manually modify neither the system description nor the profilers upon each change of process mapping. In order to demonstrate the effectiveness of our profilers, two case studies are conducted where the profiles are used for design space exploration of AES encryption and MPEG4 decoding systems.