A bi-SQUID consisting of three Josephson junctions has been shown to provide improved linearity in the voltageflux response when compared with conventional two junction DC SQUIDs. It had also been demonstrated that this improved linearity extends to SQUID arrays and SQIFs constructed using bi-SQUIDs. Experimental results for these arrays have typically been compared with results obtained from mathematical modelling since the manual creation of a complete model that can be simulated for each design is prohibitively time consuming and complex. We present a method of simulating such designs using superconducting EDA tools. Complete circuit models are obtained using the compact model extraction tool included in InductEx-LVS. These models include the Josephson junctions, inductors, resistors and all magnetic couplings from the layout. The models are simulated using JoSIM Superconductor Circuit Simulator to obtain the voltage-flux response. We discuss how the results compare with simulated results for designs that use conventional DC SQUIDs as well as with experimentally verified bi-SQUID designs from literature. Additionally, we consider the advantages and disadvantages of different flux bias application methods for 2D bi-SQUID SQIF designs