Installing SSD for boot drive, original HDD for data.

If you boot with both hard drives at the same time, depending on which is set to priority you will booth one or the other by default. IMHO, I would back up data from the 2tb hdd, and just wipe it. Registry files wont reflect on the new SSD, so installed programs wont work correctly by default if you boot from the SSD.

TLDR- Backup and wipe the 2TB HDD, love the SSD.