Sketch and libraries Storage organization

Sketch file Storage
I have a basic question about sketch file storage. When a newby like myself, first starts out with this Arduino thing, I was guided to start with Blink. So I upload Blink and am impressed. Next I modify Blink to whatever number of blinks and various delays and save them as I learn to:
Save As: myBlink, myBlink1, myBlink2, myBlink3, etc, on and on. When I save these personally modified sketches they get saved to:
C:\Users\Stephen\Documents\Arduino\myBlink
My sketch Files get saved here and then show up in Sketchbook. So eventually this Arduino folder has gotten to be so large, that it's getting difficult to find the sketch I want to load, or find my latest version of a project sketch that I've been working on. When my sketches have libraries in them and are saved, a new sub-directory of libraries is created, many times duplicating a library already included in the Arduino library, already established.
I'm getting errors like:
Multiple libraries were found for "SD.h"
Multiple libraries were found for "SPI.h"
Multiple libraries were found for "EmonLib.h"
I'm sure there must be a way to organize the Arduino sketch files and libraries to eliminate these kinds of errors, but it is overwhelming to me. Does anyone have an idea of where I can look for some ideas of how to solve this issue.

@sdingman

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Bob.