You can migrate it over, but if the HDD capacity outweights the SSD (i.e. 250GB SSD and a HDD with 300GB of space used) then it will not work.
I would recommend backing up any documents that you have and re-install what you want on your hard drive. This is because the registery is going to be on the SSD and not the HDD going forward. So just copying/pasting the folders will not work. The only thing that will be effected is programs. This is because you are going to have to change the letter drive on your HDD now.
My recommendation? Backup data on your HDD, wipe it. Install Windows on the SSD and install programs back to the hard drive.