I use the same in the bobbin as I do on top. I do my quilting on my longarm machine. I've not tried two different types as I was taught to use the same. I was told it would avoid tension problems. I would think the same would apply with a home machine. Others may not have had issues and can give you more advice.

I use cotton thread, top and bottom. Hugs..Carol

For Effect! I use two diff Threads,
If the Backing is Cream (baby quilts), I like to use Cream Polyester sewing Thread "Seralon" for bobbin. Also I switch off the auto cutter and Tuck the end threads in after.The auto cutter will leave a funny (Knotty) and colour at the back of the quilt.
I do find that the polyester Embroidery thread is better/more durable than cotton .
For Free motion I use top and bottom to match and "Isacord" Brand Thread. This will disguise some of my bad/uneven stitching.
Happy Quilting
From Bev

I use polyester thread top and bottom/Lillian

I buy my quilting threat from Long Creek Mills and use the same top and bottom. It;s easier on the tension. I free motion quilt on my sewing machine.
Meri