You have an emulator. An emulator takes the place of a chip so you can do very fast changes during tuning, etc., but it doesn't provide any way to actually write to a chip.

You need a prom programmer, whose sole purpose in life is to write to chips. Prom programmers have software that comes with them, so you just select the device you want to program (a 27C256 or 28C256 or whatever you're using) and select the .bin file that your tuning software generates, and it writes the bin file to the chip.

Just to make it more confusing, some programmers can be emulators also.
It really depends on the brand and model of programmer that you get, the APU1 Autoprom setup on Moates would be an example of this (I just looked, I figured there would be one there).

So you need to buy more stuff! Just what you wanted to hear, right? So you could keep the emulator, and buy a programmer, or return the emulator and buy an all-in-one unit. Depends on what you want to do and what your budget is.

Now you know why there are a lot of flash-based chip replacement daughterboards coming on the market for different applications. Many of those can do emulation, at least close to real-time, and there is no programmer involved because the flash is written during the emulation process. The Hondata K-Pro boards are like that, and there are some others for a GM and some other stuff (none of which I'm familiar with at all). It looks like Moates is coming out with one sometime soon (Demon, listed on their start page) and that should work for your ECU also.

As a side note, I haven't done any PM6 stuff for a long time, but I used to make daughterboards for the non-chip-able PM6s to allow them to be chipped with a socket and everything. I probably have a dozen or so of those boards left somewhere, I'll have to find them and sell them sometime. Not much need for OBD0 stuff anymore though, so I just stopped doing it. Most OBD0 people never wanted to actually pay for anything either, so that didn't help at all.
Oh, and the little VTEC driver boards I made that installed inside the PM6 and used the TurboEdit VTEC program. No more bitching together parts when doing a Mini-Me conversion with a PM6. Those were cool, they had all of the parts for the signal inversion, a solenoid driver, and an VTEC LED too all on one penny sized board with pins to install in the missing auto tranny lock-up solenoid location.
It was fun stuff, I don't have time for any of that stuff anymore though..