What substrate you are going to use? What application? I assume you use silicon substrate and sputtering for deposition. Deposit the bottom layer completely over the substrate. Mask the region or area with suitable masking agent and mark it. Now deposit the second layer. If you use two or four probe, you can use the bottom deposited layer as electrode 1 and masked deposition as electrode 2. Before that you must study comprehensively for the bilayer structure (effect of thickness, interface effect, strain effect, etc.)