What you have to do, is move all of your user's folders into the optibay.
Once you have Snow Leopard installed and running fine in the SSD, go over to the optibay drive, and format it/partition it as you wish.
Create directories in there, such as Downloads, Music, Documents, Pictures. Move all of your data that is currently in the SSD in those folders, into the Optibay drive.
Create a new admin account, log on as this new user.
In your optibay drive, create Aliases/softlinks for the folders you created by right clicking, in say, Documents -> Make Alias. You can now drag this alias into your User.
Now, everytime you download something, or access your photos/data, the softlink will redirect to your optibay drive.
And yes, if you don't use the data in your optibay drive, it will go to sleep after a while (provided you have set that up in Energy Saver preferences).