I fish the Wilson in the late spring through the fall for trout - lots of cutties in there. While bait is legal - I'd really advise against it when fishing for trout. You have to remember that in addition to the cutthroat - you're going to be catching salmon and steelhead smolt when going down to trout sized gear. Lures reduce the number of gut-hooks and increase the chances of the smolt by-catch surviving. It's a conservation thing.
In-line spinners and spoons are killer. I fish the 1/16th and 1/24th oz size Rooster Tails, along with similar sized Panther Martens and Blue Foxes.
When fly fishing - streamers and nymphs swung through deeper, slower stretches - or dry & dropper in shallower, rifflier sections unless there's a lot of surface action, then it's dry & dropper over any water. Standard attractor patterns and generic buggy flies work great for this. For broken, fast water, I like Humpies or Wulffs or Bivisible dry flies, sizes 10-14, with a nymph dropper a size or two smaller. Hard to beat a black or olive woolly bugger though. Dead drift it, or strip and twitch it. Buggers are like crack for trout.