The way you plan it (Install SSD > install OS > next add the HDD), the only inconvenience you can encounter is accessibility issues but you have different options to automatically have full access to the HDD.
1. You can take ownership of the HDD,
2. you can format the OS partition and the HDD will automatically turn into regular storage.
3. You could share the HDD previously to anticipate access issues and later set the same configuration as you have in the SSD.. (leaving the old OS intact)
If you have a large amount of files deleting them can be a long precess, it would be more practical to previously partition the HDD (if it's not already partitioned) and resize the partition leaving the OS in a small partition and move there all the files you may not want, and format the drive to delete everything off the OS partition.
You can partition and resize the HDD from the Windows Vista, 7, 8 Disk Manager or in Windows XP with a third party Partition Manager.