I am currently learning how to find antiderivatives using the "$u$-substitution" or "integration by substitution" method. A key component of this is setting some expression in the indefinite integral as "$u$", and then also finding $du/dx$.
How can we then write $du = dx \cdot $ (some expression)? Isn't $du/dx$ defined as the derivative of $u$ and is not a fraction?

From a simplistic viewpoint, you can view this as a convenient mnemonic: a notation that helps you remember what's true. Once you've learned that, given dependent variables $u$ and $x$ that satisfy $u = g(x)$, you can choose the antiderivatives so that
$$ \int f(u) \, \mathrm{d}u = \int f(g(x)) g'(x) \, \mathrm{d}x $$
then it is much easier to remember the rule via implicit differentiation of differentials: that $\mathrm{d}u = \frac{\mathrm{d}u}{\mathrm{d}x} \, \mathrm{d}x$.
From a deeper viewpoint, once you recognize the patterns going on here, you'll want to form a concept of a differential $\mathrm{d}x$ as a new kind of mathematical object that really exists, and is something you can manipulate.
One can then define an integral not to be the integral of a function, or as the integral of an expression with respect to one of its variables, but instead you take integrals of differentials.
From this more sophisticated viewpoint, that's what integrals are supposed to be, and that the integral you learned in introductory calculus was just a simplification that is easier to teach and requires less sophistication to discuss rigorously.