VLC shows two windows for one video
In Preferences -> Interface, check Allow only one Instance
In the VLC preferences under the Interface section check the box for Embed video in interface
For me, setting "Number of clones" = 1 fixed this exact issue
Tools > Preferences > All > Video Splitters > Clone > Number of clones = 1
In the VLC preferences under the audio tab make sure visualization is set to default. This solved my problem of the visualizer window appearing on top of the video window.