From the EMC Handbook at
http://emc.sourceforge.net/Handbook/Handbook.html
The documentation does hint that you can you can change the mapping - it's probably hidden in a config file some where.
IO Pin Function Function Function Function
Step/Dir Quadrature Two phase Four phase
D0, pin 2 X direction X CW X Phase 0 (P19) X Phase 0
D1, pin 3 X clock X CCW X Phase 1 (P13) X Phase 1
D2, pin 4 Y direction Y CW Y Phase 0 (P19) X Phase 2
D3, pin 5 Y clock Y CCW Y Phase 1 (P13) X Phase 3
D4, pin 6 Z direction Z CW Z Phase 0 (P19) Y Phase 0
D5, pin 7 Z clock Z CCW Z Phase 1 (P13) Y Phase 1
D6, pin 8 A direction A CW A Phase 0 (P19) Y Phase 2
D7, pin 9 A clock A CCW A Phase 1 (P13) Y Phase 3
C0, pin 1 B direction B CW B Phase 0 (P19) Z Phase 0
C1, pin 14 B clock B CCW B Phase 1 (P13) Z Phase 1
C2, pin 16 C direction C CW C Phase 0 (P19) Z Phase 2
C3, pin 17 C clock C CCW C Phase 1 (P13) Z Phase 3
S3, pin 15 X/Y/Z/ lim + X/Y/Z/ lim + X/Y/Z/ lim + X/Y/Z/ lim +
S4, pin 13 X/Y/Z/ lim - X/Y/Z/ lim - X/Y/Z/ lim - X/Y/Z/ lim -
S5, pin 12 X/Y/Z/ home X/Y/Z/ home X/Y/Z/ home X/Y/Z/ home
S6, pin 11 Probe Probe Probe Probe
S7, pin 10 spare spare spare spare