Using LVDS in Stratix II

Open the AE: Assignments -> Assignment Editor

In the To column, put in the name of your LVDS pins(you can use a wildcard) and choose the assignment name I/O Standard, then select the type LVDS. By assigning them to be differential, Quartus automatically assigns the (n) pin. So you only have to assign the location of the (p) pin. If you really want to, there is a way to add a differential buffer. I recommend against it since it is not necessary and makes your code less portable.

There is also a Termination assignment that allows you to choose the resitor type you want(assuming the architecture supports it). For a double-check, after your compiler open the report and go to Fitter -> Resource Section -> Input Pins/Output Pins, which give the I/O type and if a resistor is used for every pin.