The limit switches should be connected to the pins 2 4 6 of the end stops block of connectors starting from the left with the green connectors to power on the left as you look at the board.
2 - x endstop
4 - y endstop
6 - z endstop
You can verify that they are connected and working properly by using a program called pronterface from http://www.pronterface.com and connecting to your printer then sending it the command M119. If everything is correct you should get the following:
Send: M119
Recv: Reporting endstop status
Recv: x_max: TRIGGERED
Recv: y_max: TRIGGERED
Recv: z_min: open
Recv: ok