I drain my water from the sump and replace it back in there. My skimmer freaks out for a bit but I've never had a problem. How long are you letting your mixed water stand? I let mine mix with a powerhead for a minimum of 12 hours, 24 preferably.
I'm pretty low tech, no sump, just pour in water slowly. I use 5 gallon buckets to mix, but transfer it to a smaller bucket with a pouring spout for more control. I don't worry about an exact temperature match as long as I'm within a few degrees and am only doing a 10-20% water change.