Although the general principles are pretty much the same (set the relief of the neck, set the action of the strings, adjust the intonation, etc.), the short answer to your question is to set it up the best you can and learn to play the low B with a lighter touch. The longer answer involves scale length and string tension.
What Is Scale Length?
The scale length of a string instrument is the distance from the the nut to the bridge saddles, i.e. the length of the part of the string that actually vibrates when you play. Most 4-string basses have a scale length of 34", although I've seen some as short as 30". But many manufacturers and luthiers make their 5- and 6-string basses with a scale length of 35" or even 36", for the simple reason that at 34", the low-B feels too floppy and too loose, and the lower string tension means a wider vibration, which leads to the string rattling against the frets. A longer scale length mean tighter strings.
To see why this is, imagine taking a guitar and putting a capo on the first fret. You've essentially shortened the scale length of the guitar by the width of that first fret. But you've also raised the pitches of the strings by a half-step, so to compensate, you tune them all down a half-step. Now all the strings are back in tune with a shorter scale length, but because you had to tune them down to achieve that, they're all slightly looser than they were before you put the capo on.
The same principle applies in reverse. A longer scale length means tighter strings, so a 35" low B string will have slightly more tension and feel slightly less floppy than a 34" low B. Higher-pitched strings require a shorter scale length, while lower-pitched strings require a longer one---this is why basses are longer than guitars are longer than violins.
What Does This Have To Do With Setting Up My Bass?
Even a 35" low B is still probably too short for it to really feel good. You can try to get around the floppiness by using a really heavy-guage string, but even so, it's not great. The truth is that 34" is just barely long enough for the low E string, and the extra inch isn't really enough for the low B. 7-string guitars have the same problem, by the way.
So it's still floppy, and as a result, it has a very wide vibration. This means that if you play it with the same touch as on the other strings, its vibration will be wide enough to rattle against the frets unless you set up the bass to have very high action.
The problem with high action on a 6-string bass is that at the same time that the scale length is too short for a low B string, it's too long for the high C. Remember, a high C string is almost the same pitch as a guitar's D string, yet it's a heavier gauge and almost 10" longer. High C strings are under enormous tension, so high action makes them almost impossible to play (and play in tune).
The solution? Truthfully, the only really good solution is to buy a fanned-fret instrument. The idea behind fanning the frets is to give the low strings a longer scale length and the high strings a shorter one. For example, on a Dingwall 6-string bass, the low-B has a scale length of 37" (!) while the high-C has a scale length of 33.25", while a Conklin's scale lengths range from 32" to 35". Fanning the frets definitely works, but it probably doesn't help you much.
Instead, I recommend that you set up the bass with medium action -- low enough so that the C string is manageable but the B-string isn't too close to the frets (it'll still be floppy, though, you can't avoid that). And then you have to learn to adjust your plucking technique to play the B-string softer, so that the width of its vibration isn't enough to rattle against the frets. Good luck!