This chapter focuses on the principles of management in software development projects and optimization tools for managerial decision making, especially in the environment of small IT companies. The management of software projects is specific by high requirements on qualified labor force, large importance of the human capital, low level of fixed costs, and highly fluctuating product demand. This yields a dynamic combinatorial problem for the management involving considerable risk factors. The key aspects addressed here are structuring of the project team, cost estimation, and error avoidance in the implementation phase of the project. Special emphasis is put on human resource and fault-tolerant management of the project cycle. Discrete faults and continuous stochastic inputs are used to test and evaluate project variants. We have developed an online simulation tool for this purpose that facilitates findings of optimal resource structures and creation of optimal network from task relations. General principles of software project management are presented along with the analysis of the software project simulation tool in a brief case study.