The other answers are perfectly fine, but I think they might be a bit too advanced for what you're looking for (if I could read your misunderstanding correctly).
The difficulty you're having is with the fact that those two different expressions use different meanings of the products of differentials. One of them is what we call a tensor product (denoted $\otimes$) and the other is what we call a wedge product ($\wedge$). The wedge product is the antisymmetrized tensor product and it is only defined for some specific kinds of tensors, known as forms. For example,
$$\mathrm{d}x \wedge \mathrm{d}y = \mathrm{d}x \otimes \mathrm{d}y - \mathrm{d}y \otimes \mathrm{d}x.$$
(There is a chance I'm missing a proportionality factor, but I think this is the correct expression).
When writing $\mathrm{d}s^2$, what you mean is that you are writing a symmetric $(0,2)$ tensor. This means you're using the $(0,1)$ tensors $\mathrm{d}x$ and $\mathrm{d}y$ (for example) to build a larger tensor. The correct expression is
$$\mathrm{d}s^2 = \mathrm{d}x \otimes \mathrm{d}x + \mathrm{d}y \otimes \mathrm{d}y.$$
Now, when we are performing integrals, we are dealing with other types of tensors. Namely, we always integrate forms, which are completely antisymmetric $(0,q)$-type tensors (i.e., all indices are covariant). The natural product of forms is the wedge product. Hence, your last expression actually reads
$$\mathrm{d}z \wedge \mathrm{d}\bar{z} = |\det J| \mathrm{d}x \wedge \mathrm{d}y.$$
Hence, the main point in your confusion is that there are two different products of differentials written in the same way. One of them is used to build tensors, the other is used to build forms.