When you install Windows, make sure only the SSD is connected to make sure you dont accidentally install it elsewhere. Then install all your drivers and such.
Connect up the HDD, initialize and format it, should be good to go.
There is no easy solution as far as I know, you have to be vigilant when installing programs. Usually it will ask you where you want to install it, and by default it will try C: drive (Your SSD). You have to tell it to install to the HDD. Same with movies, pictures and downloads. Set up your web browser so that it downloads to the HDD, move your user files to the HDD as well.