In this work we perform molecular-dynamics simulations, both on the coarse-grained and the chemistry-specific levels, in order to study the influence of morphology on the mechanical properties of polymer nanocomposites (PNCs) filled with uniform and patchy nanoparticles (NPs). Our main aim is to provide with insights into understanding the visco-elastic and stress-strain performance of the studied systems in correlation to the morphology of filled PNCs. Through the coarse-grained model, the non-linear decrease of the elastic modulus and the maximum of the viscous modulus around the shear strain of 10% is clearly reproduced. By turning to the polybutadiene model, we examine the effect of the shear amplitude and the interaction strength among uniform NPs on the aggregation kinetics. Interestingly, the change of the storage modulus as a function of the aggregation time exhibited a maximum value at intermediate time attributed to the formation of a polymer-bridged filler network in the case of strong interaction between NPs. By imposing a dynamic periodic shear, we probe the change of the storage modulus as a function of the strain amplitude while varying the interaction strength between uniform NPs and its weight fraction. The number of neighboring fillers, the total filler-filler and filler-polymer interactions are calculated to analyze the structural evolution under shear. A continuous filler network is developed at a moderate shear amplitude, which is critically related to the interaction strength between NPs and the weight fraction of the fillers. In addition, we study the self-assembly of the patchy NPs, which form the typical chain-like and sheet-like structures. For the first time, the effect of these self-assembled structures on the visco-elastic and stress-strain behavior of PNCs is compared.