Right now all im trying to do is generate two different PWM signal lines using timer zeron, pins 5 and 6 correct?
Yes they are the output for that timer. However as mentioned above you need to use a second timer (eg. Timer 2) if you want to have the extra control over the frequency.
When specifying your own frequency the "A" side of the timer counts up to the requested top, and the "B" side of the timer counts up to the duty cycle.