The one that seems the least complicated from the perspective of what's on the page, this version of the power is also the least credible in terms of the real world. If your atoms are smaller, then you can't possible breathe oxygen, because your lungs' tiny molecules are no longer compatible with the air's bigger ones. A size-changer wouldn't be able to eat or drink either, or could, but couldn't metabolize any nutrients from it. The only way to make this work is if the hero is consistently shrinking molecules in his immediate vicinity - the air, at the very least - which could lead to some interesting practical applications; or else has a breathing apparatus, which is an interesting wrinkle in its own right.
In this version of the power, the hero can compress the space between atoms, or possibly even between particles inside his atoms. This is how the Ant-Man movie SAYS it works, though a compressed man couldn't actually ride an ant. Because the way this works, the character's mass would not change. A 180 lbs. man would still weigh as much (at 1G, of course). Inversely, a growing character with this version of the power wouldn't become a giant so much as a vaporous cloud or light balloon. (Power Pack's Mass Master is one of the few characters to actually manifest this version fully.)
As the hero shrinks, his mass is shunted to another dimension (let's call it the Pym Dimension), just as a growing character would import mass from it (and indeed, as the shrinking hero must when he returns to full size). This dimension would be nothing but conceptual mass, unless you want to imagine people being violently stripped of their atoms by an unaware hero. (A variant would have the mass come from SOMEwhere, near or far, but then you'd have to contend with some pretty spectacular chemical reactions and radiation.) Most shrinking heroes have both fewer AND denser atoms, to explain their suite of powers. Somehow, the human body works with fewer atoms, which probably speaks to a link between the self and what's been deposited in the Pym Dimension. You may have a tiny brain in the here and now, but a lot of the processing is being done elsewhere. The Atom, for example, has been able to put more "weight" into a punch by drawing from that invisible store of mass, making himself more or less heavy as situations required.
There are other ways a character could change size, but these are definitely weird. There's the proxy method, where one's mind is uploaded to a miniaturized version of oneself, like in Doctor Who's The Invisible Enemy, though that's cheating. For growing, you could do it the old-fashioned way, with cell division (which is how we grew from tiny babies to full-grown adults), but that doesn't account for shrinking back down, unless the larger body can be shed like a husk. So imagine a hero who could generate a tiny version of himself and leave his larger body behind, if you like. Or the hero could split into several selves, each using the original's total mass. The more you split, the smaller the copies.
Whatever version of the power you look at, things get real wonky when the hero shrinks down to subatomic size (even before then). Your atoms can be more densely packed, but can they contract to smaller than an actual particle? You can have fewer atoms in your body, but what happens when you're just ONE atom, or less? Perhaps "smaller atoms" is the only possible explanation, since it would theoretically allow for atoms smaller than a particle, and certainly, there's no air to breathe down there and it doesn't seem to affect anyone. Notably, the "quantum realm" makes an appearance in Ant-Man as this unexplainable place, but the very fact that it's possible to go there puts the lie to Pym's "denser atoms" theory. In the comics, the Marvel Universe proposes a Microverse, another dimension that's accessed when you go too far down. But that's cheating. Here again, the Pym Dimension is our key to understanding the true shrinking hero's ability to sit on an electron and admire the view: If one shunts ALL their mass into the Pym-D save a stray gluon or other particle building block, one is simply using that gluon as a probe into the quantum realm. The hero interprets this world into understandable images (rotating spheres, his own body, etc.), but he's physically in that other space, as mass and consciousness.
Now the real question: Is there more money to be made with the Pym Particle/Dimension from the military or as a miracle diet?