Hi Sir John,
Sorry for not defining in Full!
Please have the additional Information:
The encoder I'm using is a Magnetic encoder here >> http://didel.com/Rome.pdf
(The encoder has an on board H-Bridge and the whole system works from voltage fed between 3 to 6 volts to the encoder ,Please see the above link it's very elaborative and shows a lot of picture's) and Yes an Arduino is a NANO Arduino.
and The motor I'm using is a 6volt DC motor and the whole system is powered by a 7806 voltage regulator that gives 6 volt power coming to it from a wallwart with 1 Amp power @ 8 volt Encoder Channel 1 is connected to D2 Interrupt PIN and Encoder Channel 2 is connected to the D3 interrupt PIN on Arduino for the Motor Direction control pin's the Motor control 1 is connected to the Digital PIN 5 and Motor control 2 is connected to the Digital PIN 6 on Arduino, So this is regarding the connection's.