I don't worry much about noise.  Don't make a lot, but dont worry about every little bump.  I remember in the old days people would whisper while fishing.  Taken to ridiculous extremes where the boat makes more noise in the water than people on the boat do.  Shhhh!  You'll spook the fish.  

Being quiet is a good practice not needing any justification.  Noise to me is pollution.



Clutter is a much bigger item.  I've been the guy with a bunch of lures & a tipped over tin of worms in the boat.  The only solution is to put stuff away before the lure hits the water.  Then there's the nitty-gritty of what's a good system.

I have a small tackle box.  Plano flat box about 6"X10"X1" & a Granite Gear thwart bag.  The only items in the bilge of my canoe are paddles and my knees, maybe a water bottle rolling around.

I have heard about using a styrofoam cooler.  It doesn't work for my needs, but if you don't portage a lot then this may work for you.  Hang lures off the styrofoam inside the cooler.