I learned this the hard way and decided to share. I have a 18x36 inground pool with 2 aqua genie returns and also an automatic cover. I need to keep the water high in order to support the auto cover.
I usually drain the pool below the aqua genies to allow for ample blow out of the water. Then blow out all lines.
Here is were the big hint begins....
The aqua genies come with plastic covers to keep the water out when raising the water, yeah right.....They do not always keep ALL of the water out of the skimmer.
The problem is the returns are built inside the skimmers, if water leaks into the skimmer its going into your returns as well. Not good if you live in freezing weather like I do. I start by removing the few screws that hold the return faceplate on and remove it. I cut a piece of vinyl liner to fit perfectly into the faceplate opening (this keeps the water out). I then screw back on the face place. I also put a little antifreeze in the hole while it is open, otherwise you will never get any in through the faceplate. I then install the plastic faceplate. Put appropriate plugs in skimmer and antifreeze.
Then refill the pool to support the auto cover.
I hope this helps someone, I learned it the hard way....