I was using the separator as a separator/bubble counter.
Hence, the IN tube going into the water.
But the one problem I was having, was that the separator water would syphon back into the main(co2) bottle.
You might be able to avoid this problem by using a check valve between the two?
It seemed like it would just do it, because of the warm air(water), cooling in the main bottle at start up.
I didn't run it long enough for me to get around to figuring it all out.