Muddiness usually occurs in a mix when there are multiple lower frequencies, these tend to clash more than higher frequencies.
Do you have drums and/or multiple voices in you system that you use as bass sounds?
There are a couple of things you can try here:
- Narrow down the deep bass voices to one at a time, or mix them in one by one to see when it starts to sound muddy
- If you use multiple voices/drums in the lower frequencies, use highpass filters to filter out the lowest colliding frequencies
- Create a sidechain with you kick and bass: mult the trigger signal that triggers the kick to a AD/AR envelope, invert this envelope and set the offset to +5V, so that when the envelope is triggered the signal is moved from +5V to 0V and back. Patch the bass voice into a VCA with the CV controlled by the inverted/offset envelope, and patch this to the mix output. Now the bass gets "silenced" when the kick hits, creating a more clean mix
- Use two separate mixer modules (doesn't have to be a mixer as a lot of modules can mix signals among doing other things, MN Maths for example) and mix on your PC, as you usually have more options in a DAW for equalizing and to see at what frequency the issue occurs. Something like Expert Sleepers ES8 can work as well, you can send your separate sounds to the ES8 and mix them in a DAW.

Like mentioned in the posts above, it can also be that there's an issue with the loudness of the output from your eurorack, as these are generally way louder than normal synth/instrument volume levels. Try to decrease the volume output of your eurorack to see it if sounds less muddy.

Good luck!
-- deurstopjoris

Tons of good info here, thanks!

The side chain idea...is that a type of "ducking"?

“You must have chaos within you to give birth to a dancing star.”
― Friedrich Nietzsche