it is originally meant to be over pants, if you wanna change it so it's under pants:
go to whatever modded/vanilla pants you have (or make a new empty mod in penumbra) - advanced editing - meta manipulations - equipment parameter edits (EQP) - find the number that your pants are in glamourer (or changed items if your pants are modded; i.e. ignominy trousers are number 688) - make sure the drop-down option is "legs" when you put the number in, then add it by clicking the + - hover over the checkboxes and find "hide medium boots" -- make sure it's checked - apply changes and redraw, your pants should now be over the top of the shoes