Chipotles are available in many different forms. Typically you can find them in Mexican sections of your grocery store canned with an adobo sauce. If you are lucky then you can find them dried whole. This is the best way to get them because you can do so much more with them. If you need them hydrated, simply place a chili or two in hot water for about an hour. This makes it easier to remove the seeds and stems from the whole Chipotle. Of course you can leave the seeds in and get a bit more kick out of the pepper.
Chipotles are more than smoked, they are dry smoked and require a lot of patience and a bit of practice to make right. The traditional way to make Chipotles is by starting with a hole in the ground. A pit is filled with wood, usually pecan, though oak, hickory or fruit woods work well. The smoking time is very long, about 48 hours so you don't want a lot of strong smoke or you'll end up with some way too smoky to eat. The smoke from the fire pit feeds into a separate chamber where the Jalapeño pods are sitting on a rack. This allows airflow without too much heat. You don't want to cook the Jalapeños, just smoke them.
You can do this yourself with a backyard smoker or kettle style charcoal grill, but remember it will take about 2 days and you will need to maintain a fairly constant temperature and smoke content to get the job done right. To make your own Chipotles, start with thoroughly washed Jalapeños, without bruises or surface cuts. They shouldn't be too soft. Remove the stems and place them on the rack in your smoker or grill in a single layer. Start a small fire away from the peppers. Add presoaked wood for the smoke in small amounts. Keep the airflow low so that the fire doesn't get too hot and then continue smoking until the peppers are complete dried. It will take about 48 hours.
Chipotles are light in weight, brown in color and hard to the touch. They need to be stored in an airtight container with no moisture. You should also keep them someplace dark and cool. If you get them completely dried and keep them that way, they should last for about 12 months. Always inspect Chipotles before you cook with them. They can be ground up and used as a spice, chopped and added to sauces, soups, and any other dish, or hydrated and served on, or in most anything.
Any recipe that calls for hot peppers is a good candidate for Chipotles. The smoky flavor and the pepper's heat will add a lot to what you cook, so be careful and don't over do it.