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There are many pulse channel sounds in castlevania. To get it to sound like an instrument in castlevania, you're going to have to tweak the volume envelope and the duty cycle envelope that you're using on channels square 1 and square 2
@Diranotach: what i would suggest is simply listenig to the castlevania games' nsf (the one you have in mind) in a player like Gnsf, and single out the channel which plays the "instrument" which you like.
You can also then slow down the track's speed and realy be able to visualise where the duty changes, and how the volume modulates the sound. It has worked for me numerous times, and Famitracker emulates 100% correct as far as I know, but you may have to arrange your settings (like speed/tempo) to be able to cover your favorite tracks. The faster the tracker rolls down, the more detail can be included "between the notes".
hope it helps?