Multiple Screens Disappear Location/Reappearing

Whenever I have an external monitor connected (in a stacked manner) to my laptop, I want TotalFinder to be displayed on the lower of the monitors (my laptop). This part is fine. However, when I hide TotalFinder it goes off screen based on the top screen. TotalFinder will typically be invisible, but whenever I minimize another app or click an icon in my Dock, TotalFinder will become visible at the offset position from my top monitor. Meaning TotalFinder is visible on the top 1/3 of my bottom screen. This is horrible and extremely annoying. Can you please fix Totalfinder such that it will offset based on the screen it is assigned to.