There are several ways to prepare chipotles, but first you must begin with nicely ripened jalapeno peppers. Try to look for jalapenos that are firm without any soft spots. They should have a good, bright red color without any loose (an indication that they were picked too long ago) stems. The fresher the peppers the better the result.
One word of warning. No matter how you approach making the chipotles, you will be handling chili peppers a great deal. This means being very careful when touching sensitive areas, like your eyes. I fully recommend purchasing disposable food handling gloves before you start this project.