I have space under my monitor to hold either my customizer or my hhkb, whichever I'm not using. I do tend to leave both plugged in when I'm home, though the hhkb does travel with me.
They sit on the stand of the monitor, and on the Customizer, the monitor bezel sits over the number row, if that tells you how far it sticks out onto my desk. My desk isn't particularly deep, but it still feels like enough room to me.