From Derrick Riches,
Your Guide to Barbecues & Grilling.
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Of course the biggest ingredient to Chipotles is the smoke. You want to use a relatively mild wood for the smoke. Fruit woods are great as are hickory, oak, and pecan (the Mexican traditional wood). Make sure you have a good supply because the longer you can smoke the jalapeños the better.

It takes about 48 hours of dry heat to dry out a batch of chipotle chilies. Few people want to spend this much time smoking them so you will probably want to transfer them to another appliance to complete the drying process. This can be a food dehydrator or your oven. Either way you will want to get plenty of time in your smoker before hand. I will typically light up the smoker early in the morning and get the jalapeños smoking as early as possible on a day when I'm not going anywhere. Usually I will keep them on the smoker for about 16 hours.

Make sure that your smoker is very clean. Grease and fat drippings inside the smoker will flavor the chipotles in a way you don't want.

The trick with smoking chipotles is to avoid cooking them. Keep the fire smoky but low. You want your smoker at about as low a temperature as you can maintain while still producing smoke.

More the chilies as little as possible, but depending on your smoker you may need to rotate them around to keep an even heating.