I always use the 3 layer system, zip lock bag for individual items, or groups of, then inside a dry bag or equivalent, then i have a massive dry bag to line my bergan, on top of the bergan is a cover to keep the rain off. this is of course full proof when it comes to keeping kit dry, river crossings etc nay probs, but it all goes inside the bivi bag with your clothes which you lay/rest on when crossing...
as for wet/dirty kit, just do the reverse, keeps every thing else clean and tidy.
as for under the tarp, if im staying, its normally set up with 1 side to the ground, wood is put right at the back to dry or keep dry with emergency tinder and kindling, my roll mat is laid down with my sleeping bag inside my bivi bag on top, all my admin is done here using the wood area to lay clothes or kit as needed.
works for me very well in the woods, but on the hills it may differ due to wind conditions, but then i nearly always do winter camping....
regards.
chris.