MacOS – symbolic link not created

The quote marks are preventing ~ from being expanded to your home folder, so you need to either quote just the part with the space in it:

ln -s ~/"Foo Bar/" Foo

Note: exactly how much is quoted doesn't matter, as long as the space is in the quoted portion and the ~/ isn't. ~/Foo" "Bar/, ~/"Foo Bar"/, ~/Fo"o B"ar/ etc are all equivalent. Also, single- and double-quotes have the same effect on spaces (although they differ on other characters), so ~/'Foo Bar/', ~/Foo' 'Bar/ etc would also work.

You could also use an escape to prevent the space from being treated as a separator:

ln -s ~/Foo\ Bar/ Foo

That’s not the recommended way of configuring a two-disk OS X install. Steps:

1. Make a clean install on the SSD. Or you can just copy over the System Files. This would make steps 2 and 3 unnecessary.
2. Create a temporary admin account on the SSD.
3. Add a new account in the Users and Accounts preferences. It should match the credentials of your old account on the HDD.
4. Right click on the account after it has been created, then click on Advanced Options.
5. Set the home folder of this account as the previous home folder on your HDD.
6. Transfer the necessary apps, libraries, etc by using a disk cloning app or good old copy-pasting.

The Download folder reappears because OS X thinks that the home directory is on the SSD, not on the HDD.

Source: http://macintoshhowto.com/hardware/how-to-speed-up-your-mac-with-a-ssd-drive.html