EMC and encoders

If using EMC to run stepper motors and you want to use encoder
feedback. Are you supposed to match the encoder output count with
the steps per revolotion. Or is more pulses the merryier. At this
time i am thinking of using full step with 5mm lead screw, 2 to 1
drive reduction, and G210 full step to 10 micro step driver. The
encoder would be a 2 channel complimentry output 250 counts per rev
and 1000 counts total. I would mount this encoder on the on the
leadscrew shaft.