Put wood chunks of your choice (I use hickory) into water to soak several hours prior to cooking. I typically do this in the morning to let them get pretty well soaked by the time I get the grill going. This will allow them to smoke instead of burn.
About 2-4 hours prior to cooking, spatchcock a whole chicken. With a pair of kitchen shears, cut the chicken backbone on either side to remove it, then open the chicken so it lays flat, breast side up.
Pour the cooled marinade into a large, gallon freezer bag, then place that bag into another freezer bag (to help avoid any spills).
Place the spatchcocked chicken into the bag with the marinade, seal tightly, and make sure that the chicken is completely coated. Store in the refrigerator for 2-4 hours.
When you are close to done marinating, prepare your grill by bringing it to a roasting temperature of 300-325 degrees. If using charcoal, move coals to one side of the grill to create an indirect cooking surface. Add some wood chunks to the edges of the coals and let them start to smoke.
Remove the chicken from the marinade and place on the grill, breast side up, over indirect heat. If using a meat thermometer (highly recommended), insert the thermometer probe into the thickest part of the chicken breast.
Close the grill and slow roast for roughly 20-30 minutes, or roughly until the internal temperature has reached 120 degrees.
Flip the chicken to be breast side down and continue roasting until the internal temperature has reached 160 degrees, roughly another 20-30 minutes.
Flip the chicken one more time to be breast side up and make sure you have a nice even char on the outside. This is really just for presentation, but it looks nice :)
Roast just a bit longer until the internal temperature has reached 165 degrees. Remove and set aside to rest.
If you are roasting jalepeños, place them on the grill on more direct heat. Roast thoroughly on each side until the peppers are softened and beautifully charred on the outside. This took me about 10 minutes or so.