I Actually usually try to match the bottom thread to teh back of the quilt and the top thread to the top of the quilt.... Sometimes with many machines this causes freckling and it is not possible. SOmetimes mine will do that as well...but most of the time I can mess with my tension and get it to work.
I try to use a bobbin thread in the bobbin which is usually a bilobal polyester....a bit thinner and I use whatever teh quilt calls for on the top.