There is a Library folder but it is hidden on Lion by default when using Finder. You can see it in the terminal :
Macmini:tyr root# ls -ld Library
drwx------@ 36 tyr staff 1224 Apr 10 01:42 Library
FWIW I have a SSD + HDD setup myself and I've left my homedir on the SSD so I will still be able to login if the HDD ever fails, but I've linked all dirs containing large file to the HDD :
Macmini:tyr root# ls -l
total 1552
drwxr-xr-x 17 tyr admin 578 Mar 10 23:02 Applications
drwx------+ 5 tyr staff 170 Apr 13 02:15 Desktop
lrwxr-xr-x 1 root staff 35 Dec 31 08:15 Documents -> /Volumes/MiniHD/Users/tyr/Documents
lrwxr-xr-x 1 root staff 35 Dec 31 08:19 Downloads -> /Volumes/MiniHD/Users/tyr/Downloads
lrwxr-xr-x 1 root staff 33 Mar 18 16:11 Dropbox -> /Volumes/MiniHD/Users/tyr/Dropbox
drwx------@ 55 tyr staff 1870 Mar 16 23:06 Library
lrwxr-xr-x 1 root staff 32 Dec 31 08:19 Movies -> /Volumes/MiniHD/Users/tyr/Movies
drwx------+ 6 tyr staff 204 Feb 19 04:35 Music
drwx------+ 24 tyr staff 816 Apr 4 08:09 Pictures
drwxr-xr-x+ 88 tyr staff 2992 Apr 8 11:17 Public
drwxr-xr-x+ 3 tyr staff 102 Dec 31 08:02 Sites
lrwxr-xr-x 1 root staff 41 Dec 31 08:30 VirtualMachines -> /Volumes/MiniHD/Users/tyr/VirtualMachines
You'll notice Music isn't a link, that's because I've changed that setting in iTunes, so there's no need to replace it with a symbolic link.
Edit: creating symbolic links
(As always having a backup is essential.)
To create these kinds of symbolic links I recommend logging in as a second user then using root in the terminal. E.g. you want to create links for User1, then login as User2 and in the Terminal do :
$ sudo su -
Password:
Macmini:~ root# cd /Users/User1
Macmini:User1 root# mv Documents /Volumes/MyHDD/
Macmini:User1 root# ln -s /Volumes/MyHDD/Documents Documents
The above commands moved the "Documents" folder in the "User1" homedir to an external volume called "MyHDD", then created a link called "Documents" to the place where we moved it.
Best Answer
You can remove the bundle document type for the .download extension.
You'll have to edit /Applications/Safari.app/Contents/Info.plist and remove the entry for the download extension under Document Types. The only disadvantage to this is that, whenever Safari updates, you'll have to do this again as your changes will be overridden.
I'd also make sure you make a backup of the Info.plist file first, before you make changes, incase you move the wrong line(s) or Safari gives you any issues after making the changes.