best to get natural sea water (NSW) or premix salt water from your LFS if you need to do emergency water change. Mixing a new batch would usually take 12 hours to settle. You should purchase a good hydrometer to measure salinity. Did your ATO put too much water in or was it not working while you were away?
what!? 12 hours, not a chance. no salt takes 12 hours to mix or "settle" as you say.
. That being said, are you doing water changes with cold water? I notice you say things will hopefully improve as the temp comes up. You should always be sure to get the water very close to the same temp as your aquariums temp. 

so ask questions as you did, ther is a great support group here

