@SashaGrey My desk at work has the tower on the desk and only the power cord moves. My desk at home has the tower under it. It can't move as far up but I have more space that way.
@SashaGrey Start with the desk at max height before managing the cables so you know how much slack you need. Then it's pretty much pick where you want to run them and make sure there's nothing to catch on when moving the desk up and down.