I could very well be wrong about this, but...  Of the two red wires, one will be thicker.  If so the thicker one is power coming out of your rectifier going to you battery.  Connect it straight to the positive battery post.  The other red wire should then be 12v into the rectifier to power the system.  This should be switched 12v.  When you turn the key on, or flip the switch (whatever) you should put 12v into that wire.  Same as sending 12v to your coils.  Hopefully someone who know what they are doing will agree with me or set you straight.  Good luck and take it easy.  Julio