"Discrete audio amplifier" is a marketing phrase. It's almost impossible to know what they mean by it. It suggests that they use separate high-powered transistors for the output, but they might mean something different. Low cost receivers usually use integrated circuits for the whole amplifier. They're inexpensive but usually can't deliver as much power as amplifiers that use individual power transistors on separate heat sinks.
However, if you look closely at the specs, the 6060 does seem to have a significantly better amplifier section than the 509. (0.09%thd at 100watts compared with a much worse 0.7% for the 509)
Well the THD question is really an issue of how hard you're going to drive the unit. As Bob explained in your question below- it's really a subset of power output.
What it's saying is that the 6060 puts out 100 watts cleanly, while the 509 doesn't. The THD factor is a way to "cheat" in advertising the power output. An amplifier can really put out an oodle of power- but at some point it isn't clean power. So, manufacturers rate power output, and then let you know how clean the signal is at that point. An amplifier might be able to ouput 4000 watts, but at 50% distortion...
What they should do is set a standard THD for all power ratings, making the playing field even- but they don't.
A better way of looking at your question would be this: How much power can a unit produce cleanly? If you put the limit at .1% THD: the 6060 would put out 107 watts (guesstimate) before hitting .1%. the 509 would probably be closer to 80 watts (guesstimate) output if the limit was placed at .1% thd.
So if you try to compare apples to apples and were looking for clean output, you're looking at a 110 watt receiver vs an 80 watt unit (even though both advertise 100 watt output).
So, the question isn't necessarily how much THD you can stand- but rather how much power you want. If you plan to run the system gently, the 509 should be fine. If you want the extra headroom the power will provide, then the 6060 would be worth your investment.
Of course specs are only a small portion of the story- best bet is always to listen for yourself and decide which you like.
By discrete amps, I believe they are saying there is a dedicated amp circuit for each channel. Some lower cost amps will split the power from a single amp circuit to run both rear channels, dropping the total power output for those channels.