Case Fron panel wiring to mother board - Question

Hi,
I recently bought an MSI 648 MAX mother board and a Jupitor Sky Aluminium Case. To connect the front pannel wiring to the mother board, the mother board provides a set
of Intel compliant pin set having HDD indicator, Power, Reset and a Power Led. On thee mother board all these a 2 pins each and they are clubed together in a block of about 10 pins with pin missing(which seems normal accordiang to the diagram).
2 questions.
1. Each connecter from the Case fron panel HDD Led, power, and reset came as 2 pin connectors . Do the have specifc polarities. Meaning do' the need to be connected specicially one way or the other.
2. The last one the Power Led has 2 pins close to each other on the mother board, But the Case wiring has a a similar 3 pin connector, though only 2 wires go into it with the middle pin not connected.l This means that when I try to connect it to the mother board, one of the sockets over flow outside the motherboards pin connectors.

Is this a problem, Has anyone had this problem. What are my options.

Your help is very much appreciated.
Thanks,
Sarvi