You can create multiple canvas elements without appending them into document. These will be your layers:
Then do whatever you want with them and at the end just render their content in proper order at destination canvas using drawImage on context.
Example:
/* using canvas from DOM */
var domCanvas = document.getElementById('some-canvas');
var domContext = domCanvas.getContext('2d');
domContext.fillRect(50,50,150,50);
/* virtual canvase 1 - not appended to the DOM */
var canvas = document.createElement('canvas');
var ctx = canvas.getContext('2d');
ctx.fillStyle = 'blue';
ctx.fillRect(50,50,150,150);
/* virtual canvase 2 - not appended to the DOM */
var canvas2 = document.createElement('canvas')
var ctx2 = canvas2.getContext('2d');
ctx2.fillStyle = 'yellow';
ctx2.fillRect(50,50,100,50)
/* render virtual canvases on DOM canvas */
domContext.drawImage(canvas, 0, 0, 200, 200);
domContext.drawImage(canvas2, 0, 0, 200, 200);
And here is some codepen: https://codepen.io/anon/pen/mQWMMW