What types of problems are you having? What you are going to have to do when installing windows 7 is to use the custom/advanced options, go to the manual partition setup and erase every partition you have into free space. Then choose the SSD to install windows to. All the OS files will be installed to this drive.
When you start up windows, you are going to want to install all your programs and put all your files on the 1tb drive. Make a program files folder on your big harddrive, and anytime you install a program set that location as the installation location. It is somewhat of a pain but you are going to have to take a slight pause in your installations from now on without just breezing through next next next. Change your my documents/pictures/music/etc to the big harddrive. Now your files/programs will be on the big hd, while the os files on the ssd.