Are the batteries is a series aiding configuration              (+18v) + 9v - + 9v - (0v)

I just need to know whether to use the active or neutral wire or both

You should break the HOT with the relay contact.
However when ever possible I choose to break both (of course you would need a Double Pole relay: DPDT or DPST).

several hall effect sensors

I don't think so.

It looks like a beams of light are interruped when the shaft is rotated.
Slotted opto switches.
O/Ps would be digital high/low.

This may work in your application, take a look here (not a stepping motor though)
http://www.adafruit.com/products/1150

Just a note, sending a picture of the actual wired circuit shows us if you have overlooked something.

Simon:

What is the foward voltage you measure with a meter:
Try 5V and 100R

Review this:
http://tronixstuff.wordpress.com/2011/08/26/tutorial-maximising-your-arduinos-io-ports/

Which Arduino chip/board are you thinking of using?

Is it because a digital mulimeter isn't fast enough to show the differences as it is rapidly turning on the corresponding segments in each display and is therefore showing a higher current

Yes

With a a question like this, it is advantageous to attach a schematic diagram so it can be easily visualized (especially for us older guys).
 

Each o/p can power a driver transistor or driver chip which in turn can drive a relay.
You can use multiple extender ICs, registers that can be placed in series to extend your relay count.

Why not tell us how many relays you need to drive?

Maybe this will help:

Set up a counter, a switch identifier and a timer.

When a switch is pressed log that switch #, increment the counter and start the timer.
If the switch is pressed again increment the counter, check if the timer is still OK.
If the switch is pressed again increment the counter, check if the timer is still OK,     do something based on that switch #.

If the timer times out cancel the process.
Note: if a different switch is pressed cancel the process and start a new one.

See:    http://arduino.cc/forum/index.php/topic,45342.0.html

Your code is OK.
Maybe play with the delay.
Do you have a common ground?
Your programming technique will improve as you become more knowledgeable.

What components are you using?
Show us how your motor is wired up, a schematic, a picture.

You should include a 100nf capacitor from 0 Volts to the input pin on the voltage regulator (as close to the regulator as possible).