Looking at the manual
http://www.pololu.com/docs/pdf/0J38/jrk_motor_controller.pdf the TX and RX appear are 5 volt TTL ports.
I did not read the entire manual, but you may have to set the Jrk to serial input mode via the USB connection before you can talk to the device on the TX and RX pins. Unless you pre-set the baud rate, you must send 0xAA (decimal 170) to set autobaud before sending a command.
If this Jrk is the only Polulu device onthis serial line, I suggest that you use the Compact Protocol to simplify commands.
serout YOURPIN, T2400_4, 0xFF 'motor off
The other commands are more complex, as you're splitting a 12 bit value (0-4095) over two bytes (5 bits in command byte, 7 bits in data byte)
Example:
Set Target High Resolution
Compact protocol, binary: 110LLLLL, 0HHHHHHH
Compact protocol, hex: 0xC0 + target low 5 bits, target high 7 bits
A function that converts a 12 bit value into two bytes (5 low bits in one byte, 7 high bits in the other byte) would probably be the easiest to use solution, as other commands also use 12 bit values.
John