I have the PDF $f(x)=\frac{3}{4}(1-x^2)\mathbf 1_{-1<x<1}$ and accordingly the CDF $$F(x)=\begin{cases}0, &\phantom{-}x\le -1\\\frac{3}{4}x-\frac{1}{4}x^3+\frac12, & -1<x<1 \\1, & \phantom{-}1\le x\end{cases}$$
Since the formula for $\mathbb{E}[X]$ is the integral of $S(x)=1-F(x)$ is from $0$ to $\infty$, how do I account for the fact that $x$ is only defined from $-1$ to $1$ when I need to calculate the expectation?
Assuming that with $S(x)$ you denote $1-F(x)$, where $F$ is the CDF of $X$, then this holds only for non-negative random variables, meaning random variables that take only non-negative values. That is, if $X\ge 0$ then indeed $$E[X]=\int_{0}^{+\infty}1-F(x)dx=\int_{0}^{+\infty}S(x)dx$$This is not the case here, since your random variable $X$ takes also values in $[-1,0)$ which are obviously negative. So, you need to use the general formula of the expectation, which is $$E[X]=\int_{-\infty}^{+\infty}xf(x)dx$$ where $f$ is the PDF of $X$. This works always, for any random variable (that has a pdf $f$ of course). In your case this gives $$E[X]=\int_{-\infty}^{-1}x\cdot0dx+\int_{-1}^{1}x \cdot\frac34\left(1-x^2\right)dx+\int_{1}^{+\infty}x\cdot0dx=\frac34\int_{-1}^{1}x-x^3dx$$