How do I get the two to work together? Every once in awhile while using the Remote the transmitters lights blink but not always. I have a cd player in a closet in another room that worked with my old remote but not this one. Thanks in advance.

Here's a tutorial on setting up IR extenders, maybe it'll help.

[Link: 4electronicwarehouse.com]

What exactly is the problem, your question is very generic for anyone to provide much or a reply; you did not provide much other information either. Has the Harmony ever worked properly with your extender? What do you have to do to get the extender to respond? etc

Before I had one of the Universal brand remotes that worked with the extender but I prefer the Harmony because the Universal was never set up right.

Just set up the Harmony and sometimes the blue lights on the extender light up (randomly) but I have done nothing to try to sync or anything the two because I can't find any info about how to do so(pre looking at the mentioned website).

Even when the blue lights blink the equipment in the closet does not respond. It did with the old remote, naturally.

Sounds like just a problem with the IR strength and direction. Try using the variable outputs on the Niles at both hi and lo settings. Try repositioning the sensor and emitters. What type of wire did you use?