Unless you plan on downloading ALOT of large programs to your hard drive, and this is only a suggestion, you could just move all of your personal stuff to the 500 and keep the 40 as your main. The reason being (and Id confirm this, but) the smaller drive would make it easier/faster for your computer to find things in "program files". Then you could keep all of your pics, music, and especailly movies, etc on the larger drive. On the other hand, if you plan on loading alot of large games (COD4 all by its self is like 10GB installed) then I wouldnt suggest this, instead, partition the 500 into two 250s and ditch the 40, unless you just want to keep it for smaller stuff, maybe pics and music.
But if you can keep your "Programs" seperate from your "Personals" it does keep things running smoother.