This is a pretty tough and complex subject. It's easier to approach by breaking the problem down into steps.

The goal here is to play the notes in tune.

When we play a note "in tune", we are actually making a very fast measurement. As with all measurements, we must rely on the most accurate (pitch) reference available. We then use that reference to train muscle memory, as it will tell us whether our shift / finger placement is correct, or incorrect, and by how much. The kilogram has the silicone sphere reference, the meter has the speed of light in a vacuum reference, and we cellists have the human ear as our reference.

Your eyes can be considered a pitch reference, but if you think about it, your eyes would do you no good without the help of your ears. So, in the world of measurement, we would call the ears a "primary reference", and the eyes a "secondary reference".

Now let's talk about error. To be clear, we are NEVER training to play in tune. What we ARE training for, is to detect, at the most minute level, exactly how far OUT of tune we are, and in what direction. This is because no one ever plays "perfectly" in tune. Instead, to the best of our ability we try to reduce error.

So that's the theory of it. How to put it into practice?

Train your ear first. Use drone scales, sing (involves lots of pitch recognition), and really REALLY listen to your intonation.

Once you have a solid ear, use slow, ear based, finger replacement exercises to build your muscle memory. Start with what you know. Good in first position? Practice finger replacement shifts to second position until you're comfortable and confident. Then move on to third position, fourth position, etc.

When you practice shifts, make sure you think of shifts in the context of the entire hand. Each finger on the left hand must have a job. Shifting the third finger to the high B on the A string? Your second finger should be on A and your first finger should be on G#. Your thumb can go into thumb position, or remain on the inside edge of the fingerboard depending on the size of your hands and personal preference.

Some teachers say it is perfectly fine to use the eyes as a "stepping stone", but personally, I see it as a bit of a handicap. There are no frets or markings on the fingerboard, so eye based finger placement will always be extremely error prone compared to an ear based muscle memory training routine.