Hi Jc
If you're getting a new liner, then I would just leave the green water alone. Once the new liner is in, you will have to determine what your salt level needs to be. It looks like the salt level of the T-9 should be between 2700-3400ppm. The "Pool Math app" will give you numbers for everything you need to get the proper levels. I suggest you get the app. It is invaluable.
For your 20K pool, to get to about 3200ppm, you would need 535lbs of salt. That would be if the salt starting point of your water is 0ppm. Adding Chlorine, Muriatic acid, and other chemicals will raise salt levels by themselves. You should get a proper test kit(TF-100 is a great one), and also a salt test kit(K-1766). When the new water is in, do a salt test and then add the proper amount of salt. Do it gradually. If your pool calls for 540lbs, then add 8-9 40lb bags, brush it around, then wait a day and test salt level. Don't overshoot the level you want. If you do, then you'll have to drain a bit and add fresh water. Once you get your proper level, let it circulate for another day, then turn on the SWG. In the meantime, I would get some Liquid Chlorine to keep the water chlorinated while the salt is mixing. You should also use Liquid Chlorine to get to your intended Chlorine level, and let the SWG maintain that level. Don't rely on the SWG to bring the level up from 0.
One other note. Your T-9 is for pools up to 25000 gallons. The experts here recommend having a SWG twice your water volume, such as the T-15. Your T-9 will work for 20000 gallons, but it will need to be run much more. If you ever need to replace the T-9, I suggest upgrading to the T-15.
Good Luck!!