Organizing user home directory between SSD and HDD
Solution 1:
You can use aliases for those directories containing lots of data. Example:
/Users/you/Movies -> /Volumes/MyStuff/Movies
/Users/you/Music -> /Volumes/MyStuff/Music
/Users/you/Pictures -> /Volumes/MyStuff/Pictures
The easiest way to wipe the contents of the previous drive is to open Disk Utility, select your drive, and then select the 'Erase' tab. Choose the options you want and wait until it finishes.
Solution 2:
With the lastest version of Montain Lion, you can set up a Fusion Drive and let OS X manage where your files are at while you enjoy SSD speeds and spinning hard disk drive capacity, seamlessly. This option would be business as usual once the Fusion Drive is set up.
Create a Boot-able Backup and make sure Mountain Lion is up to date.
Create a Fusion Drive between the 64GB SSD and and the 500 GB hard drive.
Avoid manually managing what is or is not on the SSD
Do backup often, since now there are 2 things that can fail that can cause your one effective set of data to go bye bye.