I suppose we could also use the integral representation of polylogarithms $\displaystyle \operatorname{Li}_{\nu}(x) = \frac{x}{\Gamma(\nu)}\int_0^{\infty} \frac{t^{\nu -1}}{e^t - x}\,dt$ (where, $\Re(\nu) > 0$) and rewrite our integral as:
\begin{align}\int_0^{\infty} \frac{\operatorname{Li}_2(-x)}{1+x^2}\,dx &= \int_0^{\infty} \int_0^{\infty} \frac{-xt}{(e^t+x)(x^2+1)}\,dt\,dx\\&= -\int_0^{\infty} \int_0^{\infty} \frac{t}{(1+e^{2t})(1+x^2)} + \frac{te^{t}}{1+e^{2t}}\left(\frac{x}{1+x^2} - \frac{1}{x+e^t}\right)\,dx\,dt\\&= -\frac{\pi}{2}\int_0^{\infty}\frac{t}{1+e^{2t}}\,dt - \int_0^{\infty}\frac{t^2e^{t}}{1+e^{2t}}\,dt\\&= -\frac{\pi}{8}\int_0^{\infty}\frac{t}{1+e^{t}}\,dt - \frac{1}{8}\int_0^{\infty}\frac{t^2e^{t/2}}{1+e^{t}}\,dt\\&= \frac{\pi}{8}\operatorname{Li}_2(-1) - 2\sum\limits_{n=0}^{\infty} \frac{(-1)^n}{(2n+1)^3}\\&= -\frac{\pi^3}{96} - \frac{\pi^3}{16} = -\frac{7\pi^3}{96}\end{align}
where, we have used the partial fraction decomposition $$\frac{x}{(x+a)(1+x^2)} = \frac{1}{(1+a^2)(1+x^2)} + \frac{a}{1+a^2}\left(\frac{x}{1+x^2} - \frac{1}{x+a}\right)$$ in the second step.
So, I suppose a natural way to proceed with the calculation of $\displaystyle \int_0^{\infty} \frac{\operatorname{Li}_2(-x)}{1+x^\alpha}\,dx$ (where, $\alpha \in \mathbb{N}\setminus\{1\}$) might be to use partial fraction decomposition of $\displaystyle \frac{x}{(1+x^\alpha)(x+a)}$ (but I doubt the calculation would be pretty .. :P)
For example, when $\alpha = 2n \ge 4$ (even integers) we have a partial fraction decomposition: $$\frac{x}{(1+x^{2n})(x+a)} = \frac{1}{(1+a^{2n})}\sum\limits_{j=1}^{2n-2} (-1)^ja^{j+1} \frac{x^{2n-1-j}}{1+x^{2n}} + \frac{a}{(1+a^{2n})}\left(\frac{x^{2n-1}}{1+x^{2n}} - \frac{1}{x+a}\right)$$ and using the fact that $\displaystyle \int_0^\infty\frac{x^m}{1+x^n}\,dx = \frac{\pi}{n}\csc\left(\frac{\pi (m+1)}{n}\right)$ we have: $$\int_0^{\infty} \frac{x}{(1+x^{2n})(x+a)}\,dx = \frac{\pi}{2n(1+a^{2n})}\sum\limits_{j=1}^{2n-2} (-1)^ja^{j+1} \csc\left(\frac{\pi j}{2n}\right) + \frac{a\log a}{(1+a^{2n})}$$
Thus, \begin{align*}\int_0^{\infty} \frac{\operatorname{Li}_2(-x)}{1+x^{2n}}\,dx &= \frac{\pi}{2n}\sum\limits_{j=1}^{2n-2} (-1)^{j-1}\csc\left(\frac{\pi j}{2n}\right) \int_0^{\infty} \frac{te^{(j+1)t} }{1+e^{2nt}}\,dt - \int_0^{\infty}\frac{t^2e^{t}}{(1+e^{2nt})}\,dt\\&=\frac{\pi}{(2n)^3} \sum\limits_{j=1}^{2n-2} (-1)^{j-1}\csc\left(\frac{\pi j}{2n}\right) \int_0^{\infty} \frac{te^{\frac{(j+1)t}{2n}} }{1+e^{t}}\,dt - \frac{1}{(2n)^3}\int_0^{\infty}\frac{t^2e^{\frac{t}{2n}}}{(1+e^{t})}\,dt\end{align*} which may be expressed in terms of Trigamma function and Hurwitz-zeta function with,
$\displaystyle \int_0^{\infty} \frac{te^{at}}{1+e^{t}}\,dt = \frac{1}{4}\left(\psi^{(1)}\left(\frac{1}{2} - \frac{a}{2}\right) - \psi^{(1)}\left(1 - \frac{a}{2}\right)\right)$
and $\displaystyle \int_0^{\infty} \frac{t^2e^{at}}{1+e^{t}} = \frac{1}{4}\left(\sum\limits_{n=0}^{\infty} \frac{1}{\left(n + \frac{1}{2} - \frac{a}{2}\right)^{3}} - \sum\limits_{n=0}^{\infty} \frac{1}{\left(n + 1 - \frac{a}{2}\right)^{3}}\right) = \frac{1}{4}\left(\zeta\left(3,\frac{1}{2}-\frac{a}{2}\right) - \zeta\left(3,1-\frac{a}{2}\right)\right)$ where, $\Re (a) < 1$.
$2^{nd}$ attempt
This is a consequence of the nice behaviour of $dx/(1+x^2)$ under $x \mapsto 1/x$ and the dilog identity $$\text{Li}_2(-x ) +\text{Li}_2( -1/x) = -\frac{\pi^2}{6} - \frac12 \ln^2 x.$$
This gives $$\int_0^\infty \frac{\text{Li}_2(-x)}{1+x^2}dx = \int_0^\infty \frac{\text{Li}_2(-1/x)}{1+x^2}dx
\\ = \frac12 \int_0^\infty \frac1{1+x^2} \left( -\frac{\pi^2}{6}-\frac12 \ln^2 x \right)dx
\\= -\frac12 \frac{\pi^2}{6} \frac{\pi}{2} - \frac12 \int_0^1 \frac{\ln^2 x}{1+x^2} dx
\\= - \frac{\pi^3}{24}- \frac12 \sum_{n=0}^{\infty} \frac{2!\,(-1)^n}{(2n+1)^3}
\\= - \frac{7 \pi^3}{96}.$$
$\displaystyle \frac{x^{s/2-1}}{1+x^s} dx$ behaves nicely under $x \mapsto 1/x$, and that gives:
$$\large \int_0^{\infty} \frac{x^{s/2-1}}{1+x^s} \text{Li}_2(-x) dx=- \frac{\pi^3}{4} \left( \frac1{3 s}+ \frac1{ s^3}\right).$$