Timer Interrupts on Due

I'm a bit confused about the code for the startTimer function.

-What is the purpose of TC3_Handler() and how does it interact with startTimer()?
-Once startTimer() is called, how do I stop the timer(how do I disable PWM)?
-There's a few lines that I don't understand in startTimer():

        TC_Configure(tc, channel, TC_CMR_WAVE | TC_CMR_WAVSEL_UP_RC | TC_CMR_TCCLKS_TIMER_CLOCK4); <--- How does TC_Configure() work? Where can I find reference about this?
        uint32_t rc = VARIANT_MCK/128/frequency; <---------- is VARIANT_MCK the frequency of arduino DUE(84MHz)? What does rc do?
        TC_SetRA(tc, channel, rc/2); //50% high, 50% low<----sets the duty cycle? 
        TC_SetRC(tc, channel, rc);<---------- what is this line for?
        TC_Start(tc, channel);<---------------enables PWM? How does it work?
        tc->TC_CHANNEL[channel].TC_IER=TC_IER_CPCS;<----------What does this line do?
        tc->TC_CHANNEL[channel].TC_IDR=~TC_IER_CPCS;<--------What does this line do?
        NVIC_EnableIRQ(irq); <-----enables interrupt?