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 might consider transfering them to another appliance to complete the drying process. You can use either a food dehydrator or an oven. Either way you need plenty of time smoking the peppers before hand. I typically light up the smoker early in the morning and get the jalapenos smoking as early as possible. Usually, I keep them on the smoker for about 16 hours.
Make sure that the smoker is very clean. Grease and fat drippings inside will influence the flavor of the chipotles negatively.
The trick with smoking chipotles is to avoid cooking them. Keep the fire smoky but low. You want to maintain a low temperature while still producing smoke.
Move the chilies as little as possible, but depending on your smoker, you may need to rotate them to keep an even heating.