How does installing programs work when user folder moved to separate drive?

Hi everyone
I have my user folder on a separate drive from my boot drive.
I have set up a new installation of OS X on a third drive and pointed the main account's user folder on that third drive to the user folder drive.
This means that the dock that shows up when I boot off that third drive contains aliases linking to programs on the ordinary boot drive.
If I install programs on the third drive and make aliases in the dock, will that cause a conflict when I boot off the ordinary boot drive?
And if I remove from the dock aliases linking to the ordinary boot drive, will they then disappear when booted off the ordinary boot drive?
Thanks for any insight.
/p

I tried that.
1) I created a standard user account called "Test."
2) While logged in as Test I edited the sidebar. Then I logged out and back in again to confirm that the settings were retained. They were.
3) While logged in as Test I copied the user folder from SystemDisk/Users/Test to DataDisk/Users/Test.
4) I logged out of Test and logged in as Admin.
5) I changed the home directory for the Test account to /Volumes/DataDisk/Users/Test.
6) I deleted the directory at SystemDisk/Users/Test.
7) I logged out of Admin and logged in as Test.
8) I edited the sidebar. Then I logged out and back in again to see if the settings were retained. They were not.
9) I repeated steps 3-7, this time moving the home directory back to its original location at SystemDisk/Users/Test.
10) Again I edited the sidebar, logged out and logged back in again. This time the settings were retained, just as they had been before I moved the directory in the first place.
Since the functionality returns when I move the home directory back to the system disk, I've concluded that it is not due to any corruption of library files or such. It seems to be a problem with the location of home directory.
V.K., in your configuration, is the account with the moved home directory an Admin account or a Standard account? I have not tested this with an admin account and I suppose that might make a difference.

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