Hey there, Shimi.
Yes, it would work. Basically I'd recommend that you disconnect the SSHD and install Windows on your SSD as it's always recommended that you have only the drive you are installing Windows to, connected to the motherboard during the installation process. And please remember to set the SATA mode from your BIOS settings to AHCI before you install Windows on the SSD.
Once the installation is completed you can reconnect the SSHD and boot to Windows. If the computer tries to boot to Windows by using the SSHD, you'll have to enter the BIOS once again and set your SSD as the first booting option from your boot priority menu. This way whenever you turn on your computer or restart, it would always boot by using the SSD.
Once you are 100% sure that the setup is working properly, you can simply backup the important data you have on the SSHD and then reformat it. This way you'll remove the old OS and everything else and you'll have a fresh secondary storage drive.
Hope that helps. Please let me know if you have any questions whatsoever.
Boogieman_WD