When it comes to the Exmouth/Ningaloo area most fly fisho's will have their own favourite flies they always take, but the following is about as 'simplified' a selection as I can recommend.

Fishing from shore - size 1/0 or 2/0 Clousers, bucktail or synthetic, best clours = yellow over white, tan over white or olive over white, (most
species )
size 2/0 & 4/0 Fatboy's, best colours = all white or light olive, light tan or light grey over white, (queenies, trevally, cobia,
mangrove jack, cod, mackerel etc)
size 2 & 1/0 Shrimp or Crab flies, (permit, bonefish, blue bastards, spanglies etc)
Fishing from a boat - Add these two flies to the ones above
size 4/0 Deceiver, white, (burley trail fishing, mackerel, longtail tuna etc)
size 1 small Surf Candy, best colours = all white, olive over white, grey over white, (for Tuna)
Cheers
Steve