The way I do my set up's is as follows:
Step 1 Truss Rod adjustment. This is the foundation of the bass set up and must be done first. This MUST be done in playing position (don't lay the bass on the workbench because the weight of the bass wil throw off the settings). I use a capo on the first fret (on top of the fret), and then fret the neck where the neck meets the body. I use the feeler gauge blade that is .015" and put the feeler gauge under the "E" string on top of the 7th fret. If the string lifts from sliding the feeler gauge under it, the truss rod is to tight and will need to be loosened slightly. Use the appropriate allen key at the top of the neck and turn the nut counter clockwise until the feeler gauge slides under without lifting the string.
Step 2 Bridge Height adjustment. This requiers a small ruler calibrated with either 32" or 64" markings. Again this must be done in playing position. Take and place the ruler on top of the fret nearest to where the neck joins the body. Now measure the "E" string from the top of the fret to the bottom of the "E" string. You want the measurement to be 4/32". If it's to high or too low adjust your bridge saddle screws appropriately up or down. Be sure to make the same amount of turns on both of the saddles adjustment screws. If you don't you'll screw up the string spacing. Now do the "A" string to about 3 and a half 32nd of an inch. Now the "D" string slightly lower than the A string. The "G" string should be at 3/32".
Step 3 Nut Height Adjustment. Now this is done with the bass on the bench, not in playing postion. You'll need a set of nut files, and a feeler gauge. I use the feeler gauge blade that is .022". Slide the blade on top of the first fret, in between the fret and the "E" string. Now measure the distance between the top of the fret and the bottom of the "E" string. If there is a gap between the feeler gauge and the bottom of the "E" string then the nut must be cut with the appropriate nut file for the size of the string slot in the nut. The nut file size is determined by the gauge of the strings you use. Check each string individually with the .022" blade and adjust each nut slot appropriately. DON'T OVER CUT THE NUT unless you want string buzz.
Step 4 String Length Adjustment (Intonation). String length adjustment is the comparison of the open note on the string, and the fretted octave on the 12th fret. Tune all your strings as you would normally do. Then check the intonation of each string on the 12th fret. If the pitch is sharp the string must be lengthened. If the pitch is to flat then the string must be shortened. On the bottom of the bridge, use a phillips screw driver to adjust the saddle length adjustment screw to make the appropriate adjustments for each string. Then retune your bass and check the intonation again at the 12th fret. Keep doing this until the string is in tune on the open and octave notes.