I realize that the Harmony does not have ISY commands integrated as in; you cannot add an ISY device to the remote. I have the infrared version of the ISY so know that it can receive IR commands. What I can't figure out is without adding a device to the remote how do I send IR commands? Simple stuff like turn a light off when the play button is pressed. I've never used the IR component of the ISY so am really quite lost.

thanks for the help!

So further searching it looks like the use of the "Universal Devices Light" device on the harmony is what I'm looking for. I have the Harmony Elite and I don't see a Universal Devices Light device. 

Harmony has the 40 ISY IR codes pre-installed.  In other words, the harmony IR blaster will send the 40 IR codes to ISY.

If you want to more completely integrate ISY and Harmony, you need to install polyglot and the harmony node server on ISY.

Thanks. I keep bumping up against polygot. May have to bite the bullet and learn it.

Interesting; when I configure a button, select the Universal Device Light device, there are no commands?

Got it, added the non-IR device