You can perform the two-electrode test with your potentiostat.

1. In the case of the CV measurement, working electrode act as a anode when the potential is increased, where the counter electrode act as a cathode simultaneously. When the potential decreases, the working electrode acts as cathode and counter electrode acts as anode. So, there's no abrupt pairs of WE=anode or cathode and CE=visa verse. The potential difference can be shown up from the difference between the WE-RE and CE-RE pair. 

It should be noted that if the potential increases for the working electrode, the potential for the cathode decreases with absolute amount of the changes simultaneously. This will help you out to design your experimental scheme as well.

2. If you want to perform the two-electrode measurement, you should connect reference electrode line to counter electrode line. The working electrode should be the same as the three-electrode system.

You can perform the two-electrode test with your potentiostat.

1. In the case of the CV measurement, working electrode act as a anode when the potential is increased, where the counter electrode act as a cathode simultaneously. When the potential decreases, the working electrode acts as cathode and counter electrode acts as anode. So, there's no abrupt pairs of WE=anode or cathode and CE=visa verse. The potential difference can be shown up from the difference between the WE-RE and CE-RE pair. 

It should be noted that if the potential increases for the working electrode, the potential for the cathode decreases with absolute amount of the changes simultaneously. This will help you out to design your experimental scheme as well.

2. If you want to perform the two-electrode measurement, you should connect reference electrode line to counter electrode line. The working electrode should be the same as the three-electrode system.

In principle you should be only interested in the reaction occurring at the working electrode. Under this assumption it is meaningless to measure the potential difference between the working electrode and the counter electrode as it is not fixed. Usually the counter electrode is an inert surface where a redox reaction occurs with the sole aim to counterbalance the current flow due to the reaction you are interested in at the working electrode. No fixed potential is ascribable to the CE. As to the potential difference between RE and CE why are you inerested in it?

The three electrodes system allows to controll in a more rigorous manner the applied potential between WE and RE eliminating any  ohmic drop between these two electrodes simply forcing the current to flow between the CE and the WE.

The above answers are good. I will also add, if you are interested in calculating the whole cell potential (voltage between anode and cathode) for a given current, you can do as follows:

1) Using a 3 electrode setup, with the anode set as the working electrode, measure the current the flows through the system at several different closely spaced oxidizing potentials (vs the reference electrode.)

2) Without moving any of the electrodes, switch the leads to the potentiostat such that the anode (formerly working electrode) is now the counter electrode, and the cathode (formerly counter electrode) is the working electrode. Now do the same test as in (1), but using reducing potentials.

3) Find the potentials for which the magnitude of current flow through the anode is equal to the magnitude of current flow through the cathode (should be opposite sign). Then, because both potentials were measured with respect to the same reference, you can use simple arithmetic (subtraction) to find the potential difference between two electrodes required to pass that amount of current through the system.

Good luck!

You can choose if your working electrode is the anode or the cathode by setting its potential...

In three electrode setup during the electrodeposition which one is cathode and anode.