Electrochemical impedance spectroscopy (EIS) is widely used for corrosion studies and in sensor design. However, the traditional single cell EIS (SCEIS) configuration has been largely limited to laboratory testing on small panels. This study intends to develop a two cell EIS (TCEIS) configuration which will make EIS more flexible for field testing without the limitation of the size of the samples and the substrate connection. Comparison measurements between SCEIS and TCEIS were carried out with coated panels under three different accelerated weathering processes (ultraviolet (UV), salt spray, and alternating UV/salt spray). Measurements from TCEIS and SCEIS showed similar impedance spectra under the first two exposure conditions but had difficulty with the measurement from the alternating UV/salt spray. Further study showed the difficulty was from the fact that alternating weathering caused more aggressive localized damage to coating which increased the chance of severe non-uniform defects. The resultant material inhomogeneity in turn caused difficulties in the interpretation of TCEIS sensor measurement. Finite element analysis (FEA) was used to simulate the measurement with a defect in the coating system and optimize the TCEIS sensor geometry. The results showed that the TCEIS design is related to the location of the defects. Additionally, the results confirmed that the position of defects can be determined through the TCEIS measurement technique.