The flat side of the disc goes toward the flywheel. It will only fit that way. Be sure to also replace the pilot bearing and when you tighten the pressure plate. Don't over tighten it. It's best to use a torque wrench and tighten to about 18-20lbft no more. Use a star pattern like when you tighten the lug nuts on the wheels on the pressure plate.
As long as it's a high temp grease it doesn't matter about the color. Just take a file or roll up some emery paper and clean up the hole a little bit. Be sure none of the grit gets on the pressure plate.