Welcome Kristey,
I too am new to the Si family but an old timer in the art of smoking. The jalapeño has a hard skin covering the soft meat of the jalapeño. Before smoking I would get a pot of boiling water and place the jalapeños in the water for two minutes with the end removed and the seeds scraped out. I would then smoke them unstuffed for 1 hour at 250 open the smoker, remove the jalapeño poppers and stuff them, return the stuffed poppers to the smoker for another 30 minutes.
This should make a good jalapeño popper. Your smoke will get onto the jalapeño and the quick parboil will take care of the outer skin firmness. The cheese will melt fast and pick up the smoke from the jalapeño.
This appetizer doesn't need a heavy smoke flavor to be delicious. you may still need to adjust the final time, but start with the above and see what you think.
