Hey there & welcome to Tom's Hardware, @Krustation!
No matter what kind of tampering you do you with you current storage configuration, always make sure you have a backup of the files from that 3 TB HDD somewhere off-site! This is the surest way to avoid any potential data loss. Just like @Rocky mentioned, you will definitely need to unplug the hard drive from the system while installing Windows onto the SSD. This is how you will prevent the unfortunate event of OS confusion, which basically scatters your system file across all the SATA devices connected and eventually lead to some booting issues.
I believe this guide might help you with the detailed step-by-step on
Windows Install & Optimization for SSDs & HDDs.
Good luck! Hope it helps you!
SuperSoph_WD