I often use the same weight in both top and bobbin, but I've been known to use a slightly heavier weight in the bobbin than in the top. I sometimes match the color of the bobbin thread to the top, but not always. I have been fmq for many years and am comfortable adjusting both my top and bobbin tension as needed.
If you are just starting out to quilt, you will probably have a shorter learning curve if you work with a good quality 40-50 wt. thread in both the top and the bobbin and use the same color in both top and bobbin. Isacord is a good one, it's a 40 or 50 wt. polyester embroidery thread, very strong and excellent for fmq. Lots of folks use Aurifil cotton 40 or 50 for quilting.
Rob