The rising wave of attacks on communicating embedded systems has exposed their users to risks of informa- tion theft, monetary damage, and personal injury. Through improved modeling and analysis of security, we propose that these flaws could be mitigated. Since HW/SW partitioning, one of the first phases, impacts future integration of security into the system, this phase would benefit from supporting modeling security abstrac- tions and security properties, providing designers with useful partitioning feedback obtained from a security formal analyzer. In this paper, we present how our toolkit supports security modeling, automated security integration, and formal analysis during the HW/SW partitioning phase for secure communications in embedded systems. We introduce “Cryptographic Configurations”, an abstract representation of security that allows us to verify security formally. Our toolkit further assists designers by automatically adding these security representations based on a mapping and security requirements.