Is there a way to have separate docks per display?
I do not have the Yosemite but on Mavericks works as follows:


  The trick is to assign a second Space to the desktop. You do that by
  pressing the Mission Control button on your Mac keyboard (F3) or
  whatever you've assigned in System Preferences > Mission Control, and
  moving the mouse to the upper right of the display until you see a
  Plus (+) icon. Click it to create a new Space.


After you've created a second Space, your dock option will change. Now you'll see this:



Now you can assign the app to the Desktop of your choice, typically either the desktop on display #1 or display #2.