Jeff, how about some more details of your ignition setup? A block diagram showing the major components would be helpful.
I would think trying to run
external ignitors in any CDI setup would be a dangerous thing to do. They're used only in inductive ignitions to switch on/off the fairly large charging currents to the coils as signaled by the logic level outputs from the ECU. External ignitors are really just solid state relays, with some built in overcurrent/current limiting.
MSD, AEM and other CDI manufacturers have adapted their CDI boxes, so they "can" run between an ECU equipped with
internal ignitors (usually an OEM type ECU such as Motronics, etc.) and the coils, but if your ECU has no onboard ignitors (and I'm 90% sure your AEM does not), then there's certainly no reason to add external ignitors if you want to run CDI. Any good CDI box should be capable of accepting a logic level ignition signal from an ECU.
With a CDI type ignition, all the charging and energy storage is done in the capacitors of the CDI box, then the CDI box sends that charge directly to the coil in one high voltage blast (usually around 400-500v). The coil then transforms that high primary voltage by its turns ratio (usually 70:1 up to 100:1) to the secondary voltage
Ignitors aren't meant to handle high voltage, only high current, so it's no wonder yours let the smoke out
if they were between the CDI box and the coils. If they were wired between the ECU and the CDI box, in order to do a signal inversion, frankly I don't think that's necessary, because as I mentioned above, any good CDI box these days should be able to accept a logic level ignition signal from an ECU.
Another point to be very careful of, is to be sure that your coils are compatible with, and recommended for your MSD ignition. Many make the mistake of trying to use big coils with a lot of inductance on a CDI system, and subsequently smoke the coils, and/or the CDI box. You must always remember on a CDI system, the coils are only used as voltage transformers, not for energy storage.
Here's an excellent description of the CDI vs Inductive coil differences from McLaren, who build both types:
http://www.mclarenelectronics.com/Products/All/App_Act_Ign.asp
poor bugger, lucky you didn't have a shotgun handy or i can imagine you may have ventilated your car a bit more than it needs 
