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Here's code for timer 1 on a atmega32u tested in a Teensy 2.0:

void setup() {
  // put your setup code here, to run once:

   // Timer 1 Fast PWM mode *toggling* OC1A at 50kHz with *two* OCR1A counts
   // And 7.32 bits 0-159 PWM on OC1B at 100kHz
   // Output on OC1B  
   // Set at TOP, Clear at OCR1B
   // WGM =15 0b1111 

   DDRB |= bit(DDB5);
   DDRB |= bit(DDB6);
   OCR1A  = 159 ;//79;    // Set TOP count to 16000000/(2*PreScaler*Ftoggle)
                          // or 16000000/(PreScaler *Ftimer)
   OCR1B  = 10;           // 10/160 duty cycle
   TCCR1A =  bit(WGM11) | bit(WGM10) | bit(COM1A0) | bit(COM1B1)  ; // Toggle OC1A, Clear on OC1B    
   TCCR1B =  bit(WGM13) | bit(WGM12) | bit(CS10);  // Set /1 prescaler
   TCNT1 = 0 ;
}

void loop() {
  // put your main code here, to run repeatedly:

}

The trick here is using OCRxA to set the TOP value/resolution/frequency of the timer, and then using OCRxB as the PWM-controlled output. The popular examples aim for a specific frequency with toggling, but often don't go into showing the PWM with the non-TOP OCRxx registers.

If you check the registers for your chip, this should also adapt to the other timers. Here, I used timer1 to avoid confusing delay() and millis().