Hi,
The CRAMPS has space for built-in drivers, and it not itself a breakout board, so really would not be useful for your system as a hardware option. The reason I mention it is that it is a complete software setup that would be ready to run and has schematic available to see how the INI and HAL files are used with direct relation to the BBB hardware.
The CRAMPS wiring configuration is not tied to any size stepper motor (the board would be though). The CRAMPS configuration can handle up to 6 motors.
The easiest way to start using the BBB and MachineKit would be with the BBB in full "desktop" mode, using a USB keyboard, mouse and an HDMI monitor. This way you don't have to worry about trying to run through a terminal (if you meant SSH in on a remote terminal). You can use the Machinekit software running the Axis GUI to try and control your motors. Start with the CRAMPS configuration and its pinout. Use BBB pins for STEP/DIR that are specified by the CRAMPS ini and hal. This way you do not need to worry about changing the setup.sh. I would recommend one of the older versions of Machinekit software from a couple years back as they would run "out of the box" on a BBB. The newer ones may require some tweaking.
From the main linux desktop screen, open a linux terminal and type Machinekit followed by a carriage return.
A selector screen should come up and allow you to select the CRAMPS setup. Do that, and after it has initialized, it will bring up the Axis GUI.
From there you can start making your connections from the BBB pins to your motor driver. Start with only one drive and get it working before trying to add more i.e. the CRAMPS specified X STEP, X DIR and a GND pin are all you would need to use to go from the BBB to your drive (make sure your drive does not need an external enable signals to be ready to go). Then try to jog the X axis. Depending on the CRAMPS configuration (which I'm only vaguely familiar with) you may need to have a jumper wire between two BBB pins: an enable output and an enable input. You can read the HAL file to figure out which pins to jumper. I don't know if there is a setup manual for CRAMPS that describes setup of not, but without the jumper you would either have to change the HAL (not recommended to start with) or simply add the jumper. Once you get familiar with getting the X moving, you can move on to adding more axes, or start modifying the INI and HAL as necessary. Don't start modifying any of the files until you actually have something working/moving.
Jeff