You are looking at something that should be relatively straight forward.
Really, the hardware configuration shouldn't bother you too much. The Arduino has more that enough pins to accomodate all 6 led's. As such you can setup the lights in parallel, hooked up to pins on the Arduino, with a breadboard, or however you like, with corresponding resistors.
Flashing the LED's is not a problem either, it would be a matter of setting the pins high. Whenever you need to flash an LED, you simply select the pin and set it high, add a delay for the amount of time you need it to be on, and then set it low again.
Here is an example:
int led1 = 1;
int led2 = 2;
int led3 = 3;
int led4 = 4;
int led5 = 5;
int led6 = 6;
void setup () [
pinMode (led1, OUTPUT);
pinMode (led2, OUTPUT);
pinMode (led3, OUTPUT);
pinMode (led4, OUTPUT);
pinMode (led5, OUTPUT);
pinMode (led6, OUTPUT);
}
void loop () {
//will flash the led for one second, you can even put conditions on this
//(you wanted time?)
digitalWrite (led1, HIGH);
delay(1000);
digitalWrite (led1, LOW);
delay(1000);
// add for more led's as needed
}
In fact pin 13 on your Arduino should already have a built in resistor.
Now if you want to blink led's at the same time, you will have to look into things like this.
Cheers.