As I said, if everything is working ok then you have little to be concerned with. It should not matter which SATA connection the drives are connected to. I'm not 100% sure but it could be that the System Reserved partition has been created on the 2TB drive which would explain why that drive is showing as System Active, but it would usually have been named as System Reserved and only be 100MB in size. All that means is that the BCD has gone onto the 2TB drive and if you disconnect that drive it most probably won't boot.
If you are not happy with the setup, format the 2TB drive, delete its partition and disconnect it from the system, then delete the C: partition during a reinstall of Windows, that should then make the drive show the System Reserved partition has been installed on it. You can then install all your drivers and then reconnect the 2TB drive.
If you are not happy with the setup, format the 2TB drive, delete its partition and disconnect it from the system, then delete the C: partition during a reinstall of Windows, that should then make the drive show the System Reserved partition has been installed on it. You can then install all your drivers and then reconnect the 2TB drive.