Not charging after MSD 6AL installation.

i notice there was 2 wires on one end f the ballast
I don't know what the Atomic is.
The instructions I posted are from the original MSD company, Autotronics.
The 6 series does not require the ballast, but it doesn't affect its operation if its left in place. It's easier to leave it.
Basically all I can suggest is follow the original instructions for each wire.
Use the coil positive connection to turn the MSD 6 on/off.
Cover the original coil negative wire's terminal.
Connect the MSD's coil wires to the coil.
Put the ballast back in or put a jumper where it used to be.
I can't be specific about colors or numbers of wires without knowing what the car came with or has now.