You'll need to first work out what the pin connections for the motors are, and make sure they are stepper motors.
If they are bipolar motors you should find either two or four pairs of pins which have a low-ish resistance (<100Ohm). If they are unipolar you will find four pairs with a low-ish resistance, of which each pair of pairs will have a wire in common. For reference, see the picture half way down
this AstroEQ tutorial page.
Once you have identified the pin-out, you will need to map those on to the AstroEQ pins. The AstroEQ RJ11 connectors have the following pinout:
1 2 3 4 5 6
N/C A B B A N/C
In the above "A" are one coil, and "B" are the second coil. For bipolar if you have two pairs then you can connect one pair to A and the other to B, if there are four pairs you will need to work out which to pairs to connect together which is not straight forward. If you have unipolar then you will need to leave the centre pin of each coil unconnected.
It doesn't matter which end of the A coil goes to which wire (2 or 5), and which end of the B coil goes to which wire (3 or 4), just be consistent between motors. Flipping a coil around will simply change the direction the motor spins, which can be corrected for in the config utility.