Do you want to see the color changing on the bottom as well as the top? If you do then yes you should use the same thread. Some don't want their stitches seen so well, might take away from a design on the backing fabric, if that is case I would use thread that matches the back or a grey.
Personally, I like to see the color changes and to show off my stitches so I almost always match bobbin to top.
Whatever you put in the bobbin is what is going to be seen from the back. Does that make sense.
I am sure you quilt will be beautiful with whichever thread you choose