How you accomplish homing is going to depend on the type of encoders you have. If they are three channel encoders (2 quadrature signals and 1 index) you can home on the index. If they are two channel you will have to use a switch to home to. This could be an optical sensor, a hall sensor or a simple switch.
( My cnc machine uses a simple, cheap microswitch and can home with +/- 0.001" repeatability). It's common to have an upper and lower limit switch to avoid over-runs and use one of them also as a homing switch. The actual home position can be offset from the limit. For precise homing a multi-step process of backing off the switch and approaching it at a lower speed a second time is used.
With steppers, an encoder can't be used for closed loop operation (not quite true, apparently there are some very advanced motor controls that can accomplish this using DSP, phase vector modulation, and a bunch of other stuff that mere mortals like me will never understand
) so they are usually used to verify if the actual move equals the commanded move. If they are not equal the software makes a correcting move.