In this study, we consider flexible manufacturing system loading, scheduling and tool management problems simultaneously. Our aim is to determine relevant tool management decisions, which are machining conditions selection and tool allocation, and to load and schedule parts on non-identical parallel CNC machines. The dual objectives are minimization of the manufacturing cost and total weighted tardiness. The manufacturing cost is comprised of machining and tooling costs (which are affected by machining conditions) and non-machining cost (which is affected by tool replacement decisions). We used both sequential and simultaneous approaches to solve our problem to show the superiority of the simultaneous approach. The proposed heuristics are used in a problem space genetic algorithm in order to generate a series of approximately efficient solutions.