They are a transformer with two windings. However, in most ign coils the windings are tied together at one of the terminals so essentially it becomes a single coil of wire with a connection at one end and another somewhere farther up and then the third for the plug wire.

If you change the wires so the polarity is correct as shown, you get the full effect of the entire winding between ground and the HV terminal. If you don't, then essentially the bottom or primary part is out of the circuit as far as the secondary is concerned since ground is now several hundred turns of the way up. The reverse in polarity also makes the spark want to jump from the shell to the center electrode which also reduces efficiency.

The spark is more efficient when jumping from the center electrode to ground rather than other way around. Here is a brief description of how to check.http://www.fifthaveinternetgarage.com ... ips_ign_coil_polarit.html