Smoked Duck Breasts

I have had good success with smoke first sear second - I DO like the skin crisped and fat rendered afterwards. I used a stovetop smoker when I did that so it sounds like a setup similar to yours ...

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When proper smoking is done, time, temperature and humidity are key. Smoke is transferred into the meat while moisture leaves the meat. This action stops when the protein sets up on the surface of the meat and seals off the transfer process. Protein can seal off the meat either by temperature or humidity or both. So, searing the duck breast first may seal off the outside, not allowing smoke to penetrate, though if may settle on the outside. I would smoke first, monitoring the internal temperature of the duck breast, not allowing to enter into the danger zone for bacteria & pathogen formation. Once smoked, sear and finish cooking immediately. Personally, I see no reason to sear the fat. I use to smoke and cook thousands of Margret Fume and dry cure Margret Sec years ago for a company and found they were just fine without searing.