A common solution in warehouses is to provide direct access to products due to various service policies. The construction of such warehouses is quite expensive due to the extensive service roads required, but at the same time, in accordance with the Pareto principle, most of the variety of materials does not justify the provision of direct access. We believe that similar dynamics could be achieved on a smaller area with the right operation of an indirect access storage system, as if direct access were provided to all stored units. Meanwhile, the high variety of products and the low accessibility make it a challenge in selecting and implementing the right operation method. The efficiency is influenced by the layout of the warehouse, the assignment of stored units to storage locations, and the operating processes. We conducted simulations to examine these; the results will be presented here. The design of the warehouse and the stochastic material flow was not changed during the examinations; the initial arrangements of the stored materials and the procedures for their movement were built according to several aspects. This revealed how these factors affect efficiency, the computational capacity needed, and the mutual influence they exert.