First, you really only need to empty your skimmer when it's around half full to avoid overflowing. As far as curing your rock, most people say that curing it in a rubbermade container with a powerhead and heater for a few weeks is the best idea, testing for ammonia and nitrite the whole time and doing regular water changes. During this time, the water will probably smell rather foul, so change the water whenever it gets to be too much
Depending on the rock, and the dead organisms inside, it can take a couple of weeks to a couple of months to cure, but once it does, you're home free.
Alternatively, if you're not planning on putting anything in your tank for a month or more, you can actually cure it in your tank. This is what I accidentally did when my LFS
told me that their liverock was cured when it was definitely not. My ammonia went off the chart for over two weeks and dropped from 10ppm to 0 in litterally 24 hours. Nitrites also dropped off rather quickly after that. Most people wouldn't recommend this, and I really wouldn't either, but it can work if you'd rather avoid the whole curring process with the rubbermaid tub. My tank took between 6 and 8 weeks to cycle with the uncured liverock in it. It looks amazing now, and the water tests perfectly, so it's definitely feasible to do this, but if you want a quicker cycle, it's probably not the way to go.
Definitely do not wait til the very end to change the water. Do water changes ever few days. . . any experts out there that have confilcting advice? Good luck with your tank!