So, if I put a piezo buzzer on that, it would create a tone of 5000Hz?
Choosing a suitable counter and prescaler and you could get into audio frequencies. To play a tune (if that is what you want) you would need to reconfigure the counter from time to time, but you can still have it doing its stuff in the background.
Are you saying that I would have to change values like TCCR1A and OCR1A to change the frequency from like 500Hz to 10KHz? How am I supposed to know what to change them to? What causes the need to change? What causes the LED to pulse when there is nothing that sets it to a LOW value? And what do _BV and WGM12 and all that stuff mean?
I think you did a good job writing your reference but it doesn't explain everything. It states a feature, gives an example scenario, and shows a code on how that scenario could be performed (which is great, that's how it should be done) but it doesn't explain why everything is the way it is and why certain values are used, and it isn't clear what's a constant and whats a variable. For many people on these forums, they don't care - they just want to copy a code and make sure it works. But I don't like taking something unless I actually understand it. Your guide is overall informative and an easy read, but I'm going to need some extra assitance.