I don't have much fretless experience, but I do go through the same trouble with my upright.
The first thing I will do to warm up on intonation is checking 1/2 and 1st position. In that area you have a lot of fifths and octaves to work with that can tell whether you're in the right position. Check fifths and octaves against open strings, for example finger the A on the G string and check against the open D string. The same works for 1st position, I personally like to check my C on the A string and the G on the E string agains the open G string to hear how close I can get with that fifth or octave.
From then on it's mostly muscle memory, sometimes checking the above again when you do most of your playing in the "money zone".
Try to practice against drones too, that is for example let a C note ring (via audio files or a synth if you'Re old school) and play a C major scale to that. You'll hear how each of the notes intonates against the C, and adjust accordingly.
Higher up the fingerboard is where it gets tricky. I suggest the "vomit exercise", which is simply sliding along one string to hit the various notes of a scale. For example, try A minor on the G string, start on the A, slide up to the B, slide down to the A again, slide up to the C, slide down to the A again, etc and the list goes on.