Most anything you can do to conserve heat can help with your utility bill. I'm no particular fan of the bubble blankets- but I live in California.
To cut the blanket to the interior shape of you spa, I would recommend removing the spa cover and draping the blanket over the top of the shell. Most of the blankets are semi-transparent, so you could use a marker to transfer the shape on to the blanket. To cut, you would remove the blanket and place it on a piece of cardboard in an area large enough to work on it and cut along your tracing with a sharp utility knife.