The simplest solution when there are multiple containers open would be to use the most recently active window.
Perhaps Shift / Alt / Ctrl clicking (or something) could send to different containers based on the position of the window (Shift sends to the most recently active window in the top third of the screen, Ctrl on the left half of the screen and Alt the right [or vise versa for left handed configurations]). Perhaps that might not be the most intuitive implementation possible.
If a drop down box was added to container windows, you could set a specific container to receive items sent using certain click modifiers. I don't know how feasible that is, though.
