There's a lot of ways to handle it.

You can have magic still be mysterious and not understood.

You can have magic be studied scientifically, whether or not the nature of magic itself is understood.

You can have them overlap; where they can each do the same things, but differently.

You can have them mutually exclusive, where one precludes the other from functioning, or interfere with each other to some degree

That's just a limited list of possibilities, an entire novella could be done listing all the possibilities, even with tiny explanations and examples of each. The point is to show how I tend to think of magic and science as part of constructing a system to play in (be that through game play, or writing). Magic demands an answer in world building; you have to have an idea of how and why it works, and how it does or doesn't interact with real world forces. It doesn't have to be seen/known by the reader or player, but if you don't have that idea in your head, you get inconsistent results as you build, which breaks immersion.

Now, pretty much all of my fiction, be it via role play gaming, writing, and even some of my painting, have the same underlying premise regarding magic. I choose to treat magic as a fundamental force, like gravity, electromagnetic, strong & weak nuclear. I do vary it some per each application; my role play main world has magic as a partial unifier of all forces. My secondary ttrpg setting it is separate from, but can interact with the others. In my main fictional world, it's more that magic is an expression of the interaction of intelligence (deific, mortal, or universal) with the physical world, though that explanation hasn't shown "on screen" at all yet.

Originally, back in the late eighties when I started playing d&d, the seeds were planted for the world I started building in the early nineties. It was the idea that there could be a god, or gods, of magic that had power over magic itself, but couldn't totally cut the use of magic off from other gods that was the seed.

For me, rectifying that paradox meant that any god of magic must only be a filter of sorts, giving magic it's own form of intelligence, a form of personification. In turn, that meant (to me), that all the gods in my world would be similar. The god of death wouldn't be any more capable of entirely preventing or causing death with no limits because the gods aren't really controlling the forces they represent. They are that force, that "thing", but given intelligence and a face for "reasons". Those reasons changed over the years, but amounted to the universe itself being one single intelligence looking at itself infinitely.

None of my ideas are particularly new. Piers Anthony, as an example, wrote an entire series on the gods being "incarnations" of a force that can change. His incarnations of immortality series was part of the inspiration for the specific gods I chose for my worlds.

Which is tangential to magic vs science, but key to the reason why the world builder needs to know the answer, even if they never show it, or allow it to be known in-universe. If you don't have an underlying set of rules, a system in your head, you end up with plot holes and contradictions like you see in the Harry Potter books and movies. Those stories are still engaging and fun, but those holes can break immersion if you don't ignore them.

The other end of the spectrum is something like the wheel of time series, where it's very apparent that the writer had the system of magic nailed down very tight in his head, because there just aren't many contradictions in the function of magic across the series (and, tbh, not many contradictions at all, dude kept great notes apparently).

You can look at Jim Butcher's two series and see a solid middle ground, plus the Dresden version of science and magic interfering with each other to varying degrees. He has an obvious underlying set of rules, but isn't afraid to change them if the story needs it.

I find the greatest fun as a writer/DM to be had when they can both exist in their fullest forms, both interacting with and interfering with each other based on in-universe rules. My best example of that is the imagical drive (hey, it's a lame name, but I was fucking 17 when I came up with it).

It requires a fictional substance to work, called heartstone that has the property of being a magical channel, with different applications based on whether it conducts it freely, or acts more like a semiconductor. You channel magic in, and you can tune the output of the crystals to give desired effects. In the case of the drive, that's bending the space around the drive to generate faster than light travel. I've got an unfinished story of a human that learns how to run an I-drive after being abducted by aliens, even

But! That drive is still connected to otherwise normal materials and technologies (though some of the fictional bits aren't properly "science" fiction, I'm not too much of a stickler for adherence to real world physics if it gets in the way of narrative lol).

I've got magical computers too, which use the same premise of magical gear working in tandem with "real" technology to make something greater than the sum of its parts.

That's the kind of sandbox I like best when worldbuilding for myself; damn near unlimited. I tend to not like having limits beyond internal consistency. Doesn't have to be realistic here, in reality. It just has to not break immersion within the setting.

I dunno, I could go on for hours about this because it's something I'm passionate about, but I think I've already hit wall-of-text limits for anyone trying to read this on a screen.