I just finished a Christmas table runner and used a beige thread for top quilting and a mono filament (Aurifil) in the bobbin. The backing is a forest green with red berries. I was going to use the dark/smoke in the bobbin but because I was using a light color thread on the top and I didn't want dark lines on the berries, I decided to use the light/clear in the bobbin. I think the results are "ok" overall - the quilting on the top is fine and on the backing it blends in with the background but is still noticeable. The stitches on the back are shiny and I had a bit of a tension problem in a few small areas but probably not noticeable to anyone but me. I'm not sure if the smoke color would have been better and give a smoother look.
I definitely wouldn't be changing back and forth between the clear & smoke - I don't think the difference would be worth the effort. The clear will probably blend in with both lights and darks. I agree with Watson and would try on a sample to see which will work better for the look that you want to achieve.