I usually just try to keep the top and bottom colors in the same color family and/or value so I don't get pops of color from the top to the bottom or vice-versa. Usually on thicker puffier batting this is not much of a problem but on thinner batting it is more critical. For instance I just finished a quilt with Superior Threads' Rainbow in the bobbin and a medium blue and medium green on the top with a lighter weight batting with no problems.