E-commerce systems are tools meant to support the supply chain (SC), the quality of which as well as other parts of the e-commerce system largely depend on management processes representing supply chain management (SCM). The optimal way to ensure the success of SCM is to use the methods of modelling and simulation based on appropriate models and mathematical representation of a real SC. Such models are constructed with the use of process and value-chain oriented approaches or based on the concept of multi-agent systems. Different types of models in conjunction with a suitable mathematical representation allow us to perform the simulation process which outputs can help managers make suitable decisions. The paper aims at presenting contemporary approaches to the supply chain modelling within e-commerce systems. Moreover, the case study emphasized hereby is oriented to present the sample simulation approach in order to find the optimal allocation of resources which are meant to minimize shipping costs.