If you have the proper equipment available, I would always recommend using a three-electrode cell. This is especially true, as in your case, where you are studying an electrochemical reaction and want to accurately know the potentials applied in your system. A two-electrode cell will work if the currents are low enough that you don't polarize your reference electrode (and thus perturb its potential) or in situations where the cell potentials are not important, which is not your case. Consequently, my advice is to use a three-electrode cell.

If you have the proper equipment available, I would always recommend using a three-electrode cell. This is especially true, as in your case, where you are studying an electrochemical reaction and want to accurately know the potentials applied in your system. A two-electrode cell will work if the currents are low enough that you don't polarize your reference electrode (and thus perturb its potential) or in situations where the cell potentials are not important, which is not your case. Consequently, my advice is to use a three-electrode cell.

I echo the comments of Richard A Durst ,

If you want to properly analyse half-cell reactions it is important to have a stable reference electrode, suitable for the electrochemical system. It also allows you to make better comparisons with results reported in literature.

Dear Hesam,

I would like to add that the advantage of a 2-electrode configuration comes when attempting to make fast-scan cyclic voltammetry (FSCV) or high frequency impedance measurements. 3-electrode cells are not amenable to these measurements due to input-impedance associated with the reference electrode.

Therefore, if attempting to obtain speciation after CO2 reduction using FSCV, a 2-electrode system would be optimal. One can always determine the potential (calibrate) with an internal redox standard.

Dear Hesam,

welcome,

There are satisfactory answers. Howsoever i want to stress an important thing. If you want to study the performance of the working electrode, then you must use three electrode systems in order that you can get the I-V characteristics of the electrodes itself and study different electrode structures. If you want to study the overall performance of the cell you can use two electrodes only the working electrode and the counter electrode.

Best wishes