is really isnt that confusing as long as you use the api.
Go in to the MouseDestination class, and look at there sub-classes.
Mouse Destination is a super class of those above. You can see RectangleDestination click on it
the constructor support using (x,y,w,h), or a rectangle
So you could easy do
mouse.click(new RectangleDestination(bot, x, y, width, height), true);
Or if the destination of an item keeps changing. You can do
int slot = inventory.getSlot("coins");
mouse.click(inventory.getMouseDestination(slot), true);
Its all about polymorphism, learn it