I have a 2009 Harley Davidson Nighttrain which I am changing oil in and I found what seems to be at least 2 drain plugs for the oil. Is this right? One was on the frame back towards the rear tire under the pipes and one was on the other side of the bike underneath the crank case. Am I doing this correctly?

There are indeed two drains under the bike. One is for the engine oil and one is for the transmission lubricant. Since your bike is basically a Softail, the one your looking for is the one on the frame back towards the rear tire under the pipes. Follow the pipe upwards and see if it goes to the oil tank. This will verify that you have the correct drain. Just loosen the drain plug and let a drop or two of oil come out. It should be black. If it's clear and clean looking, it may be your transmission lube but I'm sure if your bike is a Softail model, this is the drain you're looking for.

Good Luck
steve