If your using the original type of flasher it shouldn't matter, they are "electro-mechanical" and work off the current draw of the lights. If it doesn't work one way reverse the wires and try again.
This is assuming your using the original style bulbs as newer style bulbs may not pull enough current and the light will most likely come on and not flash. (this will also happen if one turn signal burns out, it needs both bulbs on to pull enough current to flash)
Polarity only matters on the newer electronic flashers used with LED lights as they will burn out if plugged in the wrong way.