061201-1114 EST USA
If your incremental encoder is on a lead screw, then you need a once per revolution mark on your incremental encoder or add a second encoder that is only a once per revolution unit.
If you have a linear incremental encoder, then get one with a second channel with widely spaced marks (equivalent of once per revolution on a rotary encoder). Otherwise your need to create a very fine resolutution sensor on your axis.
Once you have the once per revolution marker, then set your coarse limit switch to normally trigger about 1/2 way between the once per revolution occurances. Now correlate the two functions for your zero reference.