many of the saved games are in your My Documents folder - others stay in the game folder. There is a user state migration tool that will help you backup your documents and profile settings.
When you install to a SSD, there are tweaks and optimizations you can do to save space on your SSD. What you really want to do is put the OS, and a few apps and games on the SSD, and everything else on the HDD. Games don't benefit much from the SSD other than quick load times for levels. There is a tool(Steam mover) that will enable you to easily move games between the HDD and SSD(it creates junction points).
You do want to backup everything you need off the HDD, and delete everything else (preferably format the partition) but like you said you need to put the backups somewhere. You could create the backups on the HDD itself, and then install the OS on the SSD (unplug the HDD during install). then copy the backup files to the SSD, format the HDD, and copy the backup files back to the HDD and then do the restore to the HDD.
Steam mover -
http://www.traynier.com/software/steammover
SSD install - http://www.overclock.net/t/1156654/seans-windows-7-install-optimization-guide-for-ssds-hdds