First check to see if you have things set up like this. http://www.pcworld.com/article/237496/the_best_of_both_worlds_an_ssd_and_a_hdd.html
Second, you need to realize that even though you install a program to the HDD, it is still going to stick a bunch of stuff in the Windows directory. That is just the way most Windows software works.
I am assuming you have a 60gb SSD as most people are opting for 120gb for this very reason.