You don't need to create SVG or DOM nodes to manipulate the shapes 
individually.. or use multiple canvas for each "layer".

The simplest way of doing it is using a library that already provides a "scene 
graph" structure ( http://en.wikipedia.org/wiki/Scene_graph ) like:

http://guryjs.org/
https://github.com/kangax/fabric.js
http://easeljs.com/

Or if your intention is to actually build everything from scratch a simplified 
description of what a scene graph should do:

- store each scene element on an Array (shape, image, etc)
- store the commands that draw each shape
- redraw every shape on the proper order and position every time it is needed

more about it:  http://en.wikipedia.org/wiki/Painter%27s_algorithm

for the paint bucket problem check: http://en.wikipedia.org/wiki/Flood_fill

good luck.

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