Dock seeks info on wrong disk

Running Mavericks on a Mac Mini.  Had some problems which I suspected were disk related so installed Mavericks on a usb disk whilst I tested the internal disk.  The usb disk was partitioned with System and Users (two partitions).  When I was satisfied with the internal disk I used CCC to create identical partitions on the internal disk, called IntSys and IntUser.
Now I discover that the Dock is at least reading info from the Users partition on the usb disk, and not from IntUser on the internal disk although it is running from the IntSys disk.  I was trying to unmount the usb disk, and the Users partition would not unmount as it was in use.  fusers showed it to be the Dock which was the problem.  I killed the program, my dock disappeared and returned a few moments later at which time I got a message that Users couldn't be unmounted.
In the end I managed to unmount Users by preparing a kill nnn command in a terminal window, unmounting in Disk Utility and running the kill command before Disk Utility had time to tell me that Users was in use.
I've checked what I could find on both IntUser and Users to see where the Dock program looks for details of how the dock should look - which is what I assume it is looking for on the usb disk - but without luck.  Have also looked in the Dock.app directory on IntSys.  The fuser command gives me this result:
james-mac-mini:~ james$ fuser /Volumes/Users/
/Volumes/Users/: 18376
james-mac-mini:~ james$ ps -ef | grep 18376
  501 18376   432   0  9:51PM ??         1:55.17 /System/Library/CoreServices/Dock.app/Contents/MacOS/Dock
  501 18697 18687   0 11:10PM ttys000    0:00.01 grep 18376
james-mac-mini:~ james$
How do I get the machine to use the Dock.app on IntSys but take the details from the IntUser disk and not the usb disk Users?
TIA

Thanks, Bob for taking the time to reply.  However, now I've looked at it, I do have a problem with your solution.  I have right-clicked on all the icons in the dock and chosen Options/Show in Finder, and in every case it has marked the file on the IntSys disk, that is to say the internal partition for the system.  I assumed that this meant that one or other of these icons was linked in some way to data on the usb disk, and the only one I could think of was VirtualBox, where I have all my virtual machines on the usb disk.  I removed VirtualBox from the dock but the usb disk can still not be unmounted or ejected.
I assume that the dock program which stops Users from being unmounted must be one which is running, and the only ones running are Finder, Mail, Safari and Firefox.  Mail is definitely not located on the usb disk.
GOT IT!  I had two symlinks to large directories on the usb disk, Movies and Pictures.  Removed these, rebooted, and I can unmount and eject Users.

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