For instance, if i am electrodepositing at -0.1 V vs. Ag/AgCl in a three electrode setup, how i will do the same deposition (same potential) at two electrode system?
If you use the chronoamperometry technique for electrodeposition, you will never need to use two electrode system. However, electrodeposition based on chronopotentiometric technique needs two electrode system.Generally, three electrode system is much easier for electrodeposition purpose.
Transforming 3-electrode system to 2-electrode system is just to merge counter and reference electrodes into one electrode. So, if you want to get the same deposition at same potential, it would be difficult as the applied potential would have shifted. Therefore, run a cv to find out the deposition potential before you start the deposition.