Timer0 and Timer2 configuration on atmega1280
I believe it's trivial to control frequency and PWM using one timer even without interrupt. You need select timer mode supporting TOP value to specify frequency precisely (16-bit timer can do it more accurately but I don't think it's so critical for LED). FastPWM is mostly sufficient hence select mode 7. OCRnA specifies frequency f=fclk/(N*(OCRxA+1)). Output pin is selected as a OCnx (x>A) and duty cycle is controlled via OCRnx (x>A) register in range (0..OCRnA). You need select correct compare output mode (how behaves output pin) but it's well specified in datasheet. There are also such issues as double buffering because there is potencial race condition as you are changing params in runtime but it's not so critical.