I don't think your issue has to do with water level. pH below 7.0 can cause the liner to become larger and introduce wrinkles. You might want to recheck your pool's capacity. 18X36 with a shallow end is probably not 36,000 gallons. Probably closer to half of that.
To answer your question, you don't have to drop the water below the returns. Drop it to the bottom of the skimmer, then blow out the returns. You do this by loosely capping them and letting them each bubble for a while before tightening them.
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