1.) This shouldn't be. All elements of the Glaze theme are set to be AlwaysOnTop, which means that applications should not be able to overlap them. If it is only one application that does this I would check that it does not have an AlwaysOnTop option that may have priority. If not, then show us a screenshot and I might be able to identify a cause.

2.) This is detailed in the readme file for the theme. Right click on the word "Glaze" in the theme and select "Read Me", then click on the link "Usage" and read point 4). For more details about the VWM read the doc for rabidvwm.