It should still run at 16 lanes of PCIe 3.0 in the second slot. But it wont really matter for performance if it runs at 8. 8 lanes of PCIe 3.0 is more than enough for a 970.
To test how many lanes it is running, download GPUz from techpowerup.com. When you run the application, go to the section that says Bus Interface about halfway down the page. Click on the "?" and select start render test. When you do, look beside the "?" and it will tell you how many lanes of PCIe 3.0 are being used.