Best way I've found so far is to create your 'deep' bassline, and give it sub with a plug-in bass exciter. This adds harmonics an octave below your original sound to give depth. (The 'albino' S/W synth is good for sub as well.)

Create a middy bassline with a bit more funk and more high-end detail.

Make sure the harmonics don't interfere in nasty ways. Use an EQ to clean things up.

If any bass sounds overlap your BD, use EQ to clean up any harmonic clashing here as well.

Tequila