Hey there, graywolf1939. Welcome to the community!
Make sure to have all other drives (besides the SSD) disconnected from the motherboard during the Windows installation process.
As for you question - it depends on how bad is the situation with your HDD. If you're unable get your files when you connect it as a secondary storage drive, you could try out data recovery software:
http://www.tomshardware.co.uk/forum/id-1644496/lost-data-recovery.html and http://pcsupport.about.com/od/filerecovery/tp/free-file-recovery-programs.htm. If that doesn't work, you could try to access the drive via Ubuntu Live USB/DVD, to see if it's properly recognized and if you can get to your files this way. However, of the data on the HDD is really valuable to you, I'd suggest that you go for a data recovery company.
Hope that helps.
Boogieman_WD