In VisiLogic (programming software - free download from www.unitronics com > Support page > Downloads), you need to select Hardware configuration (View menu, of relative icon in Ladder editor, or from Project window (the left one).
In hardware configuration you need to select first the model, then, when you click on the picture of the controller itself, you need to go to High Speed counter (HSC).
In HSC window, for the relevant HSC (for example I0,1; or I2,3, where you need ot connect your encoder A & B signals to relevant digital inputs, let's say 0 & 1), on drop down menu, you select Shaft encoder x 4. There you need ot link register (recommended ML), which will hold number of pulses. HSC will count count Up or Down according to encoder's direction.
On selected register you will receive 4 counts for each encoder's pulse - positive and negative edges of A & B signals). If your encoder gives100 pules/revolution, you will receive 400 counts on each turn. This way you will increase x 4 the resoluiton of the encoder.