Dissolved minerals are pretty much equally distributed through out the water, so it won't really matter where you drain from. It does matter how much you drain at a time. For example, if you have a 10,000 gallon pool, and you drain & replace 1,000 gallons 5x, you'll only have replaced 40% of your water, even though you've added 5,000 gallons. The reason is, on each successive partial drain, you drain part old water and part new water.
If you drain 1/3 of your water 3x, you'll replace 70% of your 'bad' water. [ (1-0.33)^3 ]
By the way, you'll be better off if you use muriatic acid instead of "pH Down" or some other form of sodium bisulfate for your acid source.
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