Hey!
Personally what I was doing was to have a glass funnel (I dont mean a separatory funnel, I mean a glass funnel that you put on the top opening), and just pouring the liquid in the funnel.
Just remember to close the separatory funnel before pouring, unless you want a big mess

Oh and, when you are going to drain the bottom layer, you need to leave the top open, so that air can come in, otherwise air needs to come from the bottom and it makes the whole pouring off much more problematic.