Hey there, @Mark!
Since you are planning to configure the storage in your newly built PC rig with an SSD and an HDD, I'd recommend you follow this tutorial about
Windows Install & Optimization for SSDs & HDDs. It will give you a step-by-step guide on how to configure everything properly. You already are aware that you should have the secondary HDD unplugged until Windows is installed & running from the SSD to avoid any potential OS confusion.
Afterwards, once you plug your secondary HDD, you should be able to access its contents without any issues. However, it's highly recommended to perform a backup beforehand, especially when you are building a new rig and tampering with the storage. Having a copy of your files will definitely give you some peace of mind as well. Once you connect the secondary HDD, make sure you
re-format it through Disk Management if it contains any old system files from a previous OS installation. Afterwards, transfer all your files back to it from the backup drive/storage device.
Keep us posted if you have more questions. Good luck!
SuperSoph_WD