I would brine the whole chicken. I would also spatchcock it for even cooking. I wouldn't worry about brining the thighs unless you want to keep them all the same flavor profile.
Don't know anything about that marinade. I would check the label for length of time to marinate.
I used water in my water pan one time. Helped keep temps stable, but had a hard time getting above 250* and was a pain to clean. I have the Terra Cotta (orange color, not shiny) planter base wrapped in foil sitting in my water pan that is also wrapped in foil. I even throw one of those cheap turkey roaster pans on top to make clean up easier.
For chicken, I take the pan completely out of the WSM, light a BUNCH of charcoal, and leave all vents wide open. Doing it this way, I can get 350-375*, sometimes a little higher. Chicken needs high heat to get good skin. Make sure you have TBS (clear smoke) before you put the chicken on or you will end up with chicken with skin that looks like a tire. Don't ask how I know. I usually use a small chunk or two of apple / cherry / pecan. Chicken absorbs smoke easily, so a little goes a long way. At 350* and above, chicken thighs only take 45 mins. A whole spatchcocked chicken will take longer, but I would say probably 90 mins max.
For chicken, I cook by temperature. I pull when breast meat is 160* and let it rest covered to climb to 165*. Thigh meat will probably be a little higher, but they are juicy so it's ok.
Can't help with the veggies. I usually grill those and not for very long. We prefer them more firm. Your tastes may vary.