I believe you use the same method as adjusting a Beretta 92 rear sights.
Shooters at the range would come to me, as NRA instructor, complaining that their new Beretta show low and to the left. We're talking in the realm of 4 to 6 inches out at 25 FEET. I'd normally take it, shoot a full magazine through it, getting them all in the black, with no difficulty, at the same distance.
I'd then proceed to tell the shooter that we need to use a hammer to make the adjustment, and ask him to place his index finger on the bench top......
I believe that would work for fretless bass. Times four of course.
the easiest method for intonating a fretless is to place your "fretting" finger in the proper location :sign13:
that aside, it is good to get the intonation adjustment reasonably close. the most reliable method I use is to measure the nut - saddle distances and an otherwise identical bass, and use this as the rough in measurement. Next I use a pencil to lightly mark the location where the fret slot would be cut for the 15th fret. I then carefully note the string at this location making sure that I am right on the mark. If the tuner shows that I am reasonably in tune with this setting I move on to the next string.
you must remember that adjusting the saddles for intonation is simply a compensation to account for the string going sharp when you press it down against a fret. because you have a fret, there is no capability to make position adjustments to correct the pitch. on a fretless you have total control over the pitch by simply adjusting your finger placement. because of this, it is not necessary to have the intonation of a fretless set as precisely as is required for a fretted bass ... and upright basses (and cellos, violins, etc ...) do not have any adjustment for intonation - it is all in the ears and hands of the performer