If you are using the DBH and RJ45 connectors, then there should be no terminators on any of the devices plugged into the DBH. The only terminator would be plugged into the next unused jack on the DBH.
Perhaps the picture below will help to show why either a 568A or 568B cable can be used.
The picture shows the wiring for just one wire of the green and orange pairs. These pairs carry the Data A and Data B signals. The first device is connected to the M1DBH with a 568A cable, while the second device is connected with a 568B cable. With 568A, the green wire connects to pin 2 of the RJ45 plug, and the orange wire connects to pin 6. With 568B, this is reversed. But since the orange and green wires are connected together at the other end of the cable where it connects to the keypad or other device, either type of cable will work. It doesn't matter which color wire goes to which of the two pins.
The only place where using the 568A pin assignments matters is at the terminator plug. The terminating resistor needs to connect to the incoming signal pins in the RJ45. Thus, the resistor connects to pins 6 and 3 of the RJ45 (the orange/white and white/orange pair). Unless you are constructing your own terminator plugs rather than using the one supplied by Elk, you shouldn't have to worry about this.