It's best to cool the sample to nearly ambient temperature. Putting it in a small dish and swirling will cool the sample fast.
The mass of the refractometer will then practically cause the small drop of liquid on the lense to equilibrate to the temperature of the refractometer. You should wait about 30s before taking a reading.
I'd take a sample of your mash tun runnings to check your efficiency. The one that matters most for batch spargers is your pre-boil gavity after you've sparged and collected all your wort in your boil kettle. Be sure to stir the kettle before taking a sample. Knowing this and your boil-off rate will ensure your original gravity is going to be very close. It's also a chance to determine if your gravity is going to be too high and some wort volume could be replaced with plain brewing water or you could dillute with some plain water and make more beer (high efficiency).
Take another sample at the end of your boil to determine your actual original gravity. I've found it's best to cool your wort, mix with the sanitized spoon I whirlpool with and then take the sample.
You can use the refractometer for determining final gravity with a conversion tool as long as you know the original gravity. It's been identical to the hydrometer readings so I've stopped using the hydrometer.