That's right, it's a prep timer.
And yes, 6 on a d6. The number of d6s you roll depends on the number assigned to your stat. If you have a 1, you roll 1d6. If you have a 2, 2d6 and so on.
The Interrupt clock is basically a countdown to when the bad thing interferes. When it fills up, the chosen interruption happens and players have to overcome that on top of preparing for their chill time.