Disconnect the original drive before doing a clean install and then make sure the new drive boots properly before reconnecting the original drive. Since you already have a 1 TB SSD can I assume you are installing an M.2 SSD?
I just bought a brand new Dell XPS 8940, with 8GB RAM, and a 1TB SATA HDD for a great price.  I run Unity to develop AR apps, so the hardware was always going to need to be upgraded.  I have Dell RAM sticks on the way, but I also bought a new 1TB SSD.  Before I go down this road, how do I ensure that the SSD gets a clean install of Windows and becomes the Boot Drive?
XPS 8940, 1TB SSD upgrade, #5