Designing trajectories for manipulation through contact is challenging as it requires reasoning of object \& robot trajectories as well as complex contact sequences simultaneously. In this paper, we present a novel framework for simultaneously designing trajectories of robots, objects, and contacts efficiently for contact-rich manipulation. We propose a hierarchical optimization framework where Mixed-Integer Linear Program (MILP) selects optimal contacts between robot \& object using approximate dynamical constraints, and then a NonLinear Program (NLP) optimizes trajectory of the robot(s) and object considering full nonlinear constraints. We present a convex relaxation of bilinear constraints using binary encoding technique such that MILP can provide tighter solutions with better computational complexity. The proposed framework is evaluated on various manipulation tasks where it can reason about complex multi-contact interactions while providing computational advantages. We also demonstrate our framework in hardware experiments using a bimanual robot system. The video summarizing this paper and hardware experiments is found https://youtu.be/s2S1Eg5RsRE?si=chPkftz_a3NAHxLq