That's what I do personally. I also do a few pre-steps before I start Rally. Dunk / drop in 4 containers of water before they get into QT. Times vary on how long, but usually no more than a few minutes each step. I scrub the corals and plugs with a toothbrush along the way.
Corals get a ~15% H2O2 dip mixed with RO water for 15-60 seconds depending on what it is. Softies I stop at 15, LPS normally 20-30 and the rest only the plug. This step definitely beats up some things... Then corals get a seachem reef dip (iodine) dip for about 30 minutes.
Then I leave inverts / corals 8-24 hours before starting Rally to make sure things are healthy. LPS/coral get pellets, general tank gets reef roids/etc along with a full dropper full of bright coral amino. QT is less than 4 Gallons.
Seneye watches the ammonia/temp/water level and I top off as needed. Tank gets a 60-80% WC (from DT) every 1-1.5 days until Rally and Seachem is done. Not sure if that defeats the Rally or not since it just says treat for at least 3 days.
The tank glows incandescent green with Rally and it's kind of creepy.
I do not have any rocks in my QT, but I do have a sponge and dose MB7. It's probably not necessary though since I watch ammonia with the seneye and try to do a WC at around 0.50-0.075.