Here is a sample project overlaying a canvas on top of Construct's main canvas.
https://www.dropbox.com/s/6lvbkhuq0uoupy3/CanvasOverlay.c3p?dl=0
There were a few additional things you needed to do so the canvas would show.
Filling the canvas
The script that creates the new canvas also fills it with some color so you can see it, it is transparent by default.
Giving the canvas an ID
The script also gives the new canvas an ID so it can be targeted with a CSS selector
Applying some styles
A stylesheet is added using the Browser plugin. The stylesheet is in the Files folder of the project.
The styles are very simple but are needed so the canvas is positioned somewhere visible. The main canvas takes up the whole screen and by default new content is appended below existing content so the new canvas was initially off screen.
The styles I used for this bare bones example just force the canvas to stick to the top right, but you can change that.