I like to keep the tube 1/2" or so above the substrate and gently move it back and forth to dislodge any small particles. I rarely have any Eco or even sand come up my siphon tube when using this method. The mulm is light enough that this method works well for me.
You may want to try a smaller size gravel vac as this allows for even less flow. I have a very small vac (1" diameter tube, about 1/4" I.D. hose) that I purchased at Wal Mart for getting between plants. It will pick up most mulm/detritus without disturbing the substrate, even sand.
I use the small siphon for cleaning the substrate, then switch to the big siphon to get the water out quickly.