Welcome to Tom's Hardware, jb173!
Good job on the upgrade with an SSD for OS and HDD for storage.
Basically, you can simply back up the data you wish to save from the HDD somewhere else and then just re-format it through Disk Management.
As for the SSD setup, you'd definitely need to perform a clean install of the OS. Just make sure you UNplug the HDD until the OS installation on the SSD is completed, otherwise you might run into some booting issues later on.
After the SSD setup is done, plug the HDD > re-format > start using it for storage.
You'd also need to move the default documents/download location from the SSD to the HDD, here's a link that can help you with that:
https://support.microsoft.com/en-us/kb/310147?wa=wsignin1.0
Here are some other helpful links with step-by-steps for SSD + HDD setup optimizations:
http://www.overclock.net/t/1156654/seans-windows-7-install-optimization-guide-for-ssds-hdds
http://www.overclock.net/t/664738/how-to-setup-ssd-boot-drive-with-secondary-hard-disc-optimization
Hope this helped! Let me know if you have any additional questions!
Good luck!
SuperSoph_WD