are the wires colored? usually colored wires are positive and black wires are ground/negative.. if they are not colored, its best to see ur motherboard pinouts in the manual to confirm.. or else, you use a good old fashioned multimeter and check it.. Better be safe than sorry!!
Polarity is important for indicator LEDs only. If you insert a connector backwards, the corresponding Power or Disk LED won't be lit, but nothing else can happen. Don't worry, it won't break anything. If it could cause problems, the connectors would be keyed.