Confused about where to use the deep litter method

I am getting my coop and run ready for my first flock of chickens and really want to do the deep litter method. I'm just confused on where to put the shavings. Does t only go up in the enclosed part of the coop? Or can it also go on the bottom section that sits on grass and has all four walls open with only the wire for walls, but does have a roof overhead? Does it also go in the UNcovered run, or do I just use woodchips or sand there? THANKS a ton!