What configuration should I use for a system that includes an ARM and an FPGA?
I can't comment on your specific application (not being a cryptography expert), however placing a processor on board with a FPGA is an exceedingly common thing to do. Mostly the reason is that you now free up FPGA space to do what FPGA is good at, while using the less expensive separate processor to do what it is good at, perhaps even faster than could be done with a soft CPU running in the FPGA. In addition, larger FPGA's can get quite expensive, compared to faster ARM's which can be fairly reasonably priced. 

Basically I think you should use the two chips, but it's hard to make a proclamation for sure without knowing details about your specific area.