You can set the position by right-clicking and going to Settings > Position and choosing the one you want. This will also set the position relative to other windows. You can fine-tune this by right-clicking the tray icon and choosing "Edit Settings...", then adding the line "LoadOrder=N" to the section of the skin whose load order you want to change, where N is some number. Skins with lower numbers appear below those with higher numbers that have the same Position setting.