Does seem an interesting concept but my approach is much simpler let me explain: the voltage goes from 0 to 5v for simplicity and I change the duty cycle of only the modulated signal. The change between two differnt modulated signal is only for making the program robust to handle more frequencies.
Regarding to your solution a fixed period to check whether timer 1 ocr1b is on to enable timer 2 com1A is a solution i tried.