Timing

If it is a short term item like salmon or chicken or you are trying to hit the safety time exactly (like with Douglas Baldwin's Guide) than you should let it come up to temperature before you start the timer to ensure pasteurization.

However, for longer cooked items or items cooked longer than their time (like a steak you're planning on cooking for two hours anyway) it really doesn't matter much.

And in your specific case I've found that the sous vide supreme comes back up to temperature pretty quickly so normally the time to reheat should be minimal.

But when in doubt just start the timer after the water is back up at the temperature you want, that will ensure safety. Also, with sous vide you don't run the risk of over cooking the item so it's better to cook something for 30 minutes longer than 30 minutes less.