When you turn on multiple panels, there is a notice that explains this. I completely ignored it originally as well, and had to have MikeChops explain it to me. I saw it again tonight when doing remote desktop support helping someone install HM.
Hold Ctrl + Right Click + Drag - to move individual panels.
I set the main/first panels (the one with the note icon) position first for one villain. Then I use the Ctrl + Right Click + Drag to move the additional panels for that villain. Then do the same for the next villain, starting with the main panel.
HM HUD Layouts Thread