If bone-in, skin-on, they're more forgiving than boneless, skinless. Depending on the size, they'll take 60-90 minutes @ 250* (small taking the least time). Use a meat thermometer to verify that they have reached a minimum of 165* internal temp (minimum recommended temp for USDA inspected poultry). I usually take dark meat with bone-in to bit over 170*...otherwise there can be slightly red meat near the bone. You can reduce the smoke chamber temp to 225* and plan on extra cooking time with more smoke flavor, but poultry doesn't really benefit from low & slow cooking, unless it is a mature (generally very large: 8-11lb) roasting hen (what we tend to refer to as a tough old bird).
The water pan can be filled with water (this aids in smoke adhering to the meat). Some, myself included, use a thermal mass in the water pan such as washed pea-gravel or sand...a couple pounds is all it takes. In the MES 1/2-1lb would probably be enough.
Smoke wood can be just about any fruit wood, but apple is great with chicken...you could use hickory as well...it's a sharper flavor with a sweet back-ground. Cherry is one of the heavier fruit woods, more suitable for beef than poultry, though in my experience works fine for chicken...used with a bit more moderation.
If your thighs are boneless, skinless, apply butter or some other form of fat (canola or olive oil), then dry rub and smoke for 30-40 minutes on open grates. Place in open foil or pan with some melted butter and lemon juice...coat them well with the butter/juice, possibly turning over once, and continue smoking until they reach finished temps.
Smoked chicken is pretty easy...just cook to temp...over-cooking chicken, especially the breast meat, dries out quickly...again, cook to temp. Now, smoked chicken with a crispy skin? That's another story...haven't mastered it, at least not with consistency, so...I'll keep working on that and let you know...LOL!!!