To encipher, the long hand is moved clockwise until it points to the character to be enciphered and it's cipher text substitution is obtained from the position of the short hand. At the end of a word, the long hand is moved clockwise to the word separator and the character at the position of the short hand is written down, too. Thus this cipher conserves the word spacing.
Note that the cipher can't encrypt double letters: They must either be omitted, separated a null or the second must replace by a null.
When using this cipher, you need to know the (mixed) cipher text alphabet and the initial positions of the pointers. Within CipherClerk's Applet's implementation, you specify the the cipher text alphabet by a key word and an algorithm how to generate the mixed alphabet (see how a substitution is generated), while the two hands point to the first letters of the alphabet.
To proceed, you may