I have not played too much with audio realism, but I hear it is a pretty damn good emulator. if that's the case, part of you "too much bass" problem might be that you have the resonance turned too far down. on the original machine, it is a lot louder and bassier with the rez down unless you have some compression on it (a la hardfloor). without the compression it can be a bit overpwering.
that being said, when using it I usually just EQ the low-end down in square-wave mode, and leave it as is in triangle mode.
werd it....mike