I use Rakarrack for live performance. I use a Behringer FCB1010 MIDI foot controller...because I use delays a lot, having tap tempo is the main reason I like having a MIDI controller... well it is also nice for turning FX on/off.
I use a music stand for the computer -- not a good solution if you're in a band where there's a lot of moving around on stage, but if you're just a "stand-in-one-place-and-play-guitar" type like me, then it's fine.
I agree the tuner is difficult -- even for guitar it's not very reliable...it works pretty well if you're using an eBow or instrument that produces a more steady tone like a violin. It's one of the things on my list to tackle with the next release, so you can look forward to that in the early part of this year...but until then, well, to be honest, I use a little $14 Korg tuner with instrument in/out and set it on the laptop next to the touchpad. That arrangement could be improved with a little velcro.
A few tips:
Play around with the MuTroMojo for funk envelope filter sounds. It's modeled roughly on the Mutron circuit, so I expect if you dial in the range and sensitivity that works well with the Bass, you will find it useful.
Sustainer is a very soft-knee compressor with an interesting curve where the compression ratio increases with the signal level. It offers something different that you might find desirable for a Bass.
Rakarrack is lacking for any kind of an arrangement dedicated to making a good fuzz, even though there is the "Fuzz" model in the StompBox effect (which is not really a great sounding fuzz...I can say that without fear of insulting the developer because I made it
) Actually the Rat and Fat Cat models are a better representation of their namesake if that kind of sound fits what you're aiming at.