In this paper we propose a decomposition approach that hierarchically integrates the batching and local search heuristics in manufacturing scheduling. The problem comprises two main interrelated stages embedded in any production-transportation supply chain, namely (i) scheduling processing of raw materials and robot's transportation operation within each individual cell, and (ii) scheduling of transportation and distribution of batches of semi-finished products between cells. Several efficient heuristic algorithms are proposed. This work has been motivated by a real-life problem of production planning for a CIM system for manufacturing of multi-component products served by robots.