I have only been quilting a few years, and I mainly do SID, quite happily, I might add. I like SID. What I do in color selection of thread is that I pick the dominate color in the quilt and go with that. I prefer to use the same color in my bobbin. My machine seems to prefer the same thread in the bobbin also.
I am sure more experienced quilters have better answers, but that is what I do.
Dina