I would suggest you use the area of the limiting half cell. Have you characterised the anode and cathode prior to assembling the biofuel cell? Which (anode or cathode) gives you higher current operating in similar conditions to the biofuel cell?
How is your electrode looking and what are you actually interested in to show?
The current density is defined as the current through a specific area. Typically for an applied system such as fuel cells, I would use the geometric area of an electrode. This engineering value helps with the estimation of the system size that I would need to get a certain current. In fuel cells connected in series(stacked), all electrodes are of the same size and current density is the same in each cell.
Furthermore, in more fundamental research where a 3D electrode such as a high surface area carbon on a substrate, is used, the total area of the carbon could be used. This value can help you optimize the carbon loading for example.