Yep, that is a problem if you try to keep the stock ignition system. There are ways to do it if you're willing to build a little circuitry.

Or you can just ditch the stock ignition system and put in a locked distributor and use the Sniper to control the timing. That is what I'd recommend. Get rid of the ballast resistor and then you can wire J1 and J2 together so you get 12v during start and run. If you want it to look stock you could use a locked out lean burn distributor and then hide the CD box somewhere behind the glove box.