Prepare your smoker according to the manufacturer’s directions. Using oak or mesquite bisquettes, achieve a steady temperature of 275 to 300°F.
Place the chiles directly on the smoker rack, or use a shallow disposable foil pan.

Place it at the cooler end of the smoking chamber or on the upper rack, if your smoker has one.

Lower the cover and smoke the chiles for 2 ½ hours, or until they are soft, brown, and slightly shrivelled.

Remove the chipotles from the smoker. In a medium nonreactive saucepan, combine them with chile puree, water, tomato paste, vinegar, brown sugar, garlic, and salt.

Set over medium heat and bring to a simmer. Cook, stirring once or twice, until the sauce is very thick, about 15 minutes. Cool to room temperature.
Transfer the chipotles to a covered storage container and refrigerate for at least 24 hours, before using. They can be refrigerated for up to 2 weeks or frozen for up to 2 months.

For Dried Chipotle Peppers:

After removing the chiles from the smoker, place them on a rack and leave them, loosely covered, at room temperature, until crisp, light, and dry, for one to two weeks, depending on the humidity. Store airtight at room temperature.