Just remember that the side dot markers for a fretless are different than the ones are for a standard fretted bass. The dots are right where the first, 3rd, 5th, etc fret lines would be and not like the dots of a fretted bass which would be in the middle. Once I had that eureka moment, everything clicked
I had a custom fretless by Tom Clement who is a builder out of Florida. He makes some beautiful basses and I really loved the thing but it was 34" scale and at the time, I only had 35" scale basses so my intonation was starting to suffer since I was used to playing a larger scale bass. One day, I will have another fretless but right now I just can't justify it.