1) Attach _only_ the SSD to the system and install Windows 7, following all of the suggestions in the fairly recent article on getting the most out of your SSD.
2) Now attach the storage drive and boot. If the drive already has data, you should see it. If the drive is new, you will have to initialize, partition, and format
3) As described in the article, point My Documents and other data directories to the HDD. When you install iTunes or whatever, set the storage directories to locations on the HDD.
4) Have fun.