Sorry for the delay replying!
A lot depends on where the 'muddiness' is coming from. tone is affected by lots of things, from the age of your strings and your technique to the quality of the signal path. If you don't have particularly high quality processing/effects gear, try to keep the recording as clean as possible, so you can experiment with shaping the sound with plugins once you've captured the performance you're happy with.
Panning can help to put things at different places in the stereo field, and selective EQ can get rid of frequencies that don't need to be there. Also, making sure that there's a crossover on any reverb you use so it's not just generating rumble is a good idea.
It's tough to diagnose accurately without hearing and seeing you play. It may help to take your problem to a local teacher. Failing that, I teach via Skype so you could book a lesson in to address these things
Steve
— Steve Lawson: Bass 2.0 — the soundtrack to the day you wish you'd had