It's two different things on your pellet smoker, as on most pellet machines. Some brand new models are eliminating that feature, because it's confusing to so many.
Cook mode thermostatically controls temp to a set point by feeding potentially large amounts of pellet and running fan high for lots of O2. Your pellets provide the most heat (but not smoke) that way. (Some smoke, but mostly fire and heat. It has to do with the chemistry and thermodynamics of wood.) In fact, if you set your Cook mode for temps over 300F, you'll probably detect quite little smoke flavor. Set it low, and you'll get more smoke. But not as much as in....
...Smoke mode...which feeds pellets at a slow rate so they simmer, producing the most smoke. However your temperature will slowly drop that way. With my MB (using stock fan speeds and box insulation, which I have since mod'ed) I could only run in smoke mode for a half hour before the temperature dropped to a point I felt was compromising food safety. So I'd repeatedly set it for 15 minute smoke mode runs. Not a problem if you get distracted, because when the timer runs out it reverts to Cook mode controlling to your set point. When I dont' want to do much baby-sitting, I just set cook mode to 180F of so for several hours, then up it to 260F or so to finish off the meal.
I set my Cook mode time to >10 hours because I don't want it just turning off before the meat is cooked. Instead I use meat thermometers with a remote display to let me know when it's time to pull the meat.
How to set Cook and Smoke modes is all described in the MB manual. Info too on customizing Smoke mode via P-settings too. Hope I've motivated you to hunt yours down (or download another) and read it.