Anyways, currently I have what looks to be the male ISO connector with all my wiring. Now I understand that will just plug into the empeg's female ISO connector (correct?)

I don't know exactly what you have, but a complete illustrated instruction of how the ISO connector fits into the scheme is Right here.

but what do I do for the remote turn on...

That should be connected to the remote turn on lead of your stereo amplifier.

would you suggest I splice the wire before the male ISO connects to the female ISO on the empeg, or after the female?

That's totally up to you, and how you think it would be easiest to work on it after-the-fact.