Does millis() conflict with the PWM pins associated with timer 0? I've read that the millis() function uses the same timer as a couple of PWM pins. 

If you're using those PWM pins, will millis() still return the correct value?
They do not conflict as millis() strictly reads the immediate value in TCNT0 whereas PWM via timer 0 uses the hardware's ability to compare the value of TCNT0 with the values in OCR0x without affecting the value of any of them.