The popupbox is because there's multiple things at that mouse position and it doesn't know which one you wanted to click on.
To get rid of the box, select which of the options you want and then continue whatever you were doing.
I often set large components to "locked" as this stops them from coming up as a option when you click within their bounds.
Like a connector which takes up a large area you want to route tracks through/under
"Locked" also stops you accidentally moving them around which is useful.
Unless i misunderstood your problem?
Also, there's probably a keyboard shortcut to toggle the component layer so you can edit tracks without components getting in the way.
Anyone know it?