I recon you are probly just layering up to many fx in one go, and then trying to compensate by over EQ'ing, its easily done, I switched my method about 2 years ago, and it helped massivly - i dont resample any more, its an awsome way to work, but i prefer to keep things live so i have more control - now I may have 4-10 channels of bass sounds (or more when i'm in experimental mode!), each slightly diffrent, or very diffrent, whatever I feel is needed, each one may have only a few FX on them:
filters (in the synth) > distortion > modulation > saturation/color > EQ sculpting > (saturation/distortion) > compression > gentle corrective EQ and High/Low filtering
and thats about it, maybe a few bits extra here and there if i feel like it needs it
once I have my main sound sorted, i often duplicate it, and then either tweek the FX for a subtle texture change, or rip bits out and replace them with sumthing else, always remebering to re-do the corrective EQ - layering things up like that really helps to fatten the sound up, without having to bounce down and loose the ability to tweek things if its needed later....and it almost certainly is needed, the more layers you add, the more carefully you have to tweek things
Having layers like that, means you can EQ each channel so that it fits only into a certain frequency range, so you can have all your layers filling the space up, and, well, fat as fuck, and completly under control - this doesnt neccesarly mean hard cutting the low or high freqz, it could just be for eg having one channel with a 1db boost @ 1khz and a 1db cut @ 1.5khz, and another with a 1db boost @ 1.5khz and a 1db cut @ 1khz, and then a final one with a boost at 400hz - arbitrary numbers btw, experiment to find what works best
Once I have a big fat sound nicely layered up, then i work on surgical EQ on the whole group of bass channels, you can either group them, or route into a single channel, wotever your DAW allows you to do - just dont over do it, Its always worth checking the harmonic octaves of any freq you EQ out (just double up the Freq) - often harmonics can be the sneeky culprit of muddyness and over compensation, espcially lower down (kick area, snare area and the mud zone around 300hz +/- 100hz)
sometimes you might find that you cant eq the group only, so you need to go back and tweek the EQ on each channel with surigical or gentle methods