If the mix was bad it's because the mix was bad. That's more of an engineer issue and a tone/eq issue, as well as an arrangement issue to some extent (especially with a lot of low left hand stuff in the keys).
There's no right or wrong way to use the B string. I use it both for low notes and to be able to play higher up the neck without shifting around as much.
As far as getting tones evened out, I finally just got a set of balanced strings for my 6 string. Since it's tuned all in 4ths, the string gauges are pretty close to proportional (as are the frequencies of each open string. They're still close to new, but at least so far I'm really liking them more than a standard set. Typical bass string sets seem to go really heavy especially on the A and D strings for no apparent reason. The result of this seems to be a lot more low mids in the sound, which can definitely contribute to muddiness. Then the E and B strings are often a bit too light, which can result in flabbiness. Having that smooth gradation of gauges/tensions seems to smooth all that out a bit. And they feel pretty good too. The gauges I went with for B to G are 130, 100, 75, 55, 40, you'll probably have to order online if you want to do that, because GC and most other stores suck for bass strings, but especially extended range basses. I went to basstringsonline.com for mine and they were run of the mill DAddario nickels.
Also regarding strings, if you play with dead ass strings and/or with your treble rolled way off or bass really boosted, it can definitely create a lot of mud in the mix. MOST bass players (I say this as a bass player and live sound engineer) don't realize that they need a lot more highs in their onstage sound than they probably realize. Because in the audience, as soon as you get a little ways off axis from the cab (or the PA), you lose a lot of what highs are there, and all that's left is a few hundred Hz and below basically. So you don't want too much in the lows or too little in the highs. And if you're going for more of a flatwound thuddy sound, you probably need to cut around 80-100 Hz or so and boost maybe around 800-1500 to add some definition. It may not sound amazing soloed or in the stage mix, but in the room it will be a lot better and more defined. Honestly it should probably seem like it's too bright to you on stage.
There's no right or wrong way to use the B string. I use it both for low notes and to be able to play higher up the neck without shifting around as much.
As far as getting tones evened out, I finally just got a set of balanced strings for my 6 string. Since it's tuned all in 4ths, the string gauges are pretty close to proportional (as are the frequencies of each open string. They're still close to new, but at least so far I'm really liking them more than a standard set. Typical bass string sets seem to go really heavy especially on the A and D strings for no apparent reason. The result of this seems to be a lot more low mids in the sound, which can definitely contribute to muddiness. Then the E and B strings are often a bit too light, which can result in flabbiness. Having that smooth gradation of gauges/tensions seems to smooth all that out a bit. And they feel pretty good too. The gauges I went with for B to G are 130, 100, 75, 55, 40, you'll probably have to order online if you want to do that, because GC and most other stores suck for bass strings, but especially extended range basses. I went to basstringsonline.com for mine and they were run of the mill DAddario nickels.
Also regarding strings, if you play with dead ass strings and/or with your treble rolled way off or bass really boosted, it can definitely create a lot of mud in the mix. MOST bass players (I say this as a bass player and live sound engineer) don't realize that they need a lot more highs in their onstage sound than they probably realize. Because in the audience, as soon as you get a little ways off axis from the cab (or the PA), you lose a lot of what highs are there, and all that's left is a few hundred Hz and below basically. So you don't want too much in the lows or too little in the highs. And if you're going for more of a flatwound thuddy sound, you probably need to cut around 80-100 Hz or so and boost maybe around 800-1500 to add some definition. It may not sound amazing soloed or in the stage mix, but in the room it will be a lot better and more defined. Honestly it should probably seem like it's too bright to you on stage.