First check relief in the neck by holding the lowest string down on the 2nd fret with your fretting (left) hand. Then, hold the same string down on the 12th fret with your plucking thumb and tap on the string in the middle to see how straight the neck is. There should be no more than the thickness of a business card between the string and the frets. If there is no relief in the neck, a little pressure in the middle of the neck (after adjusting the trussrod wheel) should help.
The standard string gauge is .45-.100 with a .130 on the low "B" for the 5 string at 440 tuning. If you decide to tune down, typically you would increase the gauge for every 1/2 step downward that you tune. This will keep most of the measurements close by having more tension on the neck.
Factory String heights for a 4 string bass are: Bass side 3/32" to 7/64" Treble side: 5/64" to 7/64" from the top of the 12th fret to the bottom of the string. The rest of the strings should have the radius of the fretboard when looking at the top of the string, (with the A string hidden from view by the E string, etc.), rotating the bass at the same time. The "right" string height is, of course, ultimately determined by your playing style.
The same holds true for 5 string basses except the low B is set to 7/64".
For the Bongo 6 set the C string to 2/32".
If you have a single pickup bass set the pickup height to 6/32" from the plastic pickup cover to the bottom of the G string. Adjust the bass side of the pickup to be level with the pickguard.
If you have a dual pickup bass set the bridge pickup to the specs above. Follow the same procedure for the neck pickup except set that to 8/32".
For triple pickup basses you'll set the bridge and neck pickups to the specs above. The middle pickup is set to 7/32".
If fret buzz occurs from the open to the fifth fret, the neck needs more relief. If it buzzes between the 5th fret and the 12th fret, the neck needs to be straighter (turn the wheel slightly clockwise). If it occurs all over the neck, the string height need to increase (by turning the trussrod wheel slightly counter-clockwise).
For intonation: Compare the harmonic to the fretted note at the twelfth fret. If the fretted note is sharp, you need to make the string longer by turning the saddle screw clockwise, and vice versa. Make sure that the strings are coming off of the saddle straight and not in an arch. All measurements must be rechecked after each adjustment.