Artwork on a Transparent Art Board

I’m trying to do something very simple yet can’t seem to figure it out.
I’d like to work with my vector graphic line drawing on a completely transparent background. My goal is to add color in blocks behind the line drawing.
I know how to import my artwork, placing it on the art board, and then make a Live Trace. And I understand how converting it into Live Paint will create outlines. But it looks like if I want to remove the default color of the art board (White), I need to also remove the color of the line. And I don’t want to have to re-color all of my line.
I remember in the old days of Streamline how this was possible. (My last version of Illustrator was the original CS, so I’m way behind.) It looks like the only option for coloring artwork in CS4 is to do it exactly inside the lines, super-clean. And I’d like the freedom to paint behind the line.
Does anyone have a work-flow that they could share with me to achieve a line drawing on a transparent background with a second layer underneath for color?
Thank you.

Win 7, Illustrator CS5, plenty of RAM & ROM
I am having trouble with PNG transparent files also. This work is from an original EPS, so no tracing is involved. I wish to use the file in PowerPoint so I need the transparency. As I mentioned above, I thought that PNG files were natively transparent, unless you add a coloured background.
I have tried flattening the file but this does not work.
Only saving as a web file maintains the transparency, but this quality is too poor to use.

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