It's usually best to do a clean install when possible. Format the drive that you are going to install Win 10 on (usually drive C). If doing this with a USB thumbdrive, make sure you can boot from it. You don't have to do anything with your second drive. Windows won't mess with it.
I did a fresh install of Win 10 on my 6 year old Toshiba Portege two days ago. It went without a hitch. I then updated to Windows Creators with no problem. So far everything seems to be working. Windows found all the needed drivers for my system except for software for the 'Fn' key which brings up a setup menu.
Your experience may be different, so make sure you can round up all the needed drivers for your system.