How to generate a double PWM with a microcontroller?
If you really want to do it with two PWMs, you can use two timers and an AND gate to combine the output.

If you want to blink the LED as you explain in your question, it is simpler to:


Control LED brightness with a times in PWM mode
Using another timer, or even the same timer, setup an interrupt that updates PWM registers to turn the LED ON/OFF


Say you want to PWM it at 1 kHz to control brightness. So you got a timer which cycles at 1kHz and outputs a PWM signal. Now, enable the interrupt for this timer, and the interrupt handler will run 1000 times per second. In the code, increment a variable, you got a millisecond tick counter. You can use that to turn the LED on and off.

Depending on your micro, your software framework might already have a timer interrupt that already runs every millisecond, so you just need to add your code to it.