You can smoke the jalapenos just the way they are now. I like to reduce the overall drying time, so I cut off the tops and slice the chilies open. This will let the smoke get inside and out of the jalapenos, absrbing more smoke flavor. Opening up the chilies allows the moisture to get out of the peppers and speeds up drying time.
Removing the membrane and seeds from the inside of the jalapenos will reduce the heat. If you want the peppers hot, leave it intact, just be careful handling them so you don't lose too many of the seeds.