You might want to try Voxengo's GlissEq. With that eq you can use spectral overlay with two sounds to find out exactly where they cancel each other out/muddy up.

Load one instance on say kickdrum and one instance of the plugin on bass and the two spectra will be represented with a different colur each for both channels in one instance. I reckon a screenshot will explay this better:



http://www.voxengo.com/product/glisseq/

In that screenshot i reckon the blue line is the kickdrum's spectrum and the greenish one is the bassline.