It depends on your set-up really. In my last larger system (90g, 29g sump, 18g Fuge) I always did the water change from the sump. My system was designed around this method from day one and worked perfectly until the tank was taken down. Below are the details:
I had the DT on a closed loop system for W/C so that the coral up near the water's surface was never fully exposed to air. Not because the air would hurt the coral (some coral are adapted to being exposed to air during extreme low tides) but the top coral were really close to my Metal Halide lights and with no water over them they would cook in a matter of very few minutes.
I would hit MAINTENANCE MODE on my ProfiLux which in turn would turn OFF the return pump and the heaters in the sump but left the rest of my system operating. This isolated my Sump and Fuge from the DT completely. I would simply drain the desired amount of water from the sump, vac the bottom of the sump (this was the low spot where the majority of detritus settled out of the system) and then add back the same amount of freshly mixed (aerated and brought up to tank temp previously) salt water.
If I needed to clean anything in the DT I did so directly before the W/C and added a filter sock to the drain side of the fuge and let my system run like this for 15 minutes or so. All of the suspended "junk" would get pulled out and into the overflow and collect in the filter sock. This was a rare situation as I was fortunate and the tank was pretty well self maintaining in that regard.
As always YMMV