MacMini with new SSD startup drive

I have recently added an external 256G SSD drive to use as a boot drive with my mac mini. I installed a new system on the SSD and added a user with the same name etc as that on the existing internal hard drive. After booting from the new drive in Users & Groups I used Advanced options to select the Home Folder on the internal drive. I had loaded Applications to the SSD and expected all files etc to be saved, downloaded etc to the internal drive.
That sort of happens but I find the I now have two conflicting Desktops. The desktop that I see with all of the icons (i.e.not in a window) is that of the internal HD. The desktop that appears in the Sidebar is that on the SSD. Choosing Desktop as asave location in dialog boxes sometimes gives me the internal drive, sometimes the SSD.
What should I do to ensure that there is only one Desktop, and that it will be consistent across all applications, sidebar etc.
Thanks

Whew, no idea why it'd be inconsistent!???
Next time it happens click on the Apple icon at top left & see which drive it thinks it's booted from.

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