The function
$$f\left(z\right)=\frac{z^6}{\left(z^4+a^4\right)^2}$$
Has the following poles of order 2:
$$ z(k)=a \exp\left( \frac{\left(2k+1\right)}4 i\pi \right)$$
$f$ is even, therefore: $$\int _0^{+\infty }\frac{x^6}{\left(x^4+a^4\right)^2}dx =\frac{1}{2}\int _{-\infty }^{+\infty \:}\frac{x^6}{\left(x^4+a^4\right)^2}dx$$
$$\int _0^{+\infty }\frac{x^6}{\left(x^4+a^4\right)^2}dx=i\pi \sum _k\:Res\left(f,\:z\left(k\right)\right)$$
$$Res\left(f,\:z\left(k\right)\right)=\lim _{z\to z\left(k\right)}\left(\frac{1}{\left(2-1\right)!}\left(\frac{d}{dz}\right)^{2-1}\frac{z^6\left(z-z\left(k\right)\right)^2}{\left(z^4+a^4\right)^2}\right)$$
$$z^4+a^4=z^4-z_k^4\implies\dfrac{z^6(z-z_k)^2}{(z^4+a^4)^2}=\dfrac{z^6}{(z^3+z_k z^2+z_k^2 z+z_k^3)^2}$$
$$Res\left(f,\:z_k\right)=\lim _{z\to \:z_k}\left(\frac{d}{dz}\left(\frac{z^6}{\left(z^3+z_kz^2+z_k^2z+z_k^3\right)^2}\right)\right)$$
$$Res\left(f,\:z_k\right)=\frac{2z_kz^5\left(z^2+2z_kz+3z_k^2\right)}{\left(z^3+z_kz^2+z_k^2z+z_k^3\right)^3}=\frac{2z_k^6\cdot 6z_k^2}{\left(4z_k^3\right)^3}$$
$$Res\left(f,\:z_k\right)=\frac{12z_k^8}{64z_k^9}=\frac{3}{16z_k}$$
$$\int _0^{+\infty }\frac{x^6}{\left(x^4+a^4\right)^2}dx=\frac{3i\pi }{16a}\sum _{k=0}^n\:e^{-\frac{\left(2k+1\right)}{4}i\pi }$$
We consider only the residues within the upper half plane, that is to say those corresponding to $k=0$ and $k=1$.
$$\int _0^{+\infty \:}\frac{x^6}{\left(x^4+a^4\right)^2}dx=\frac{3i\pi \:}{16a}\left(e^{-\frac{i\pi }{4}\:\:}+e^{-\frac{3i\pi \:}{4}\:\:}\right)$$
$$\int _0^{+\infty \:}\frac{x^6}{\left(x^4+a^4\right)^2}dx=\frac{3i\pi \:}{16a}\left(\frac{\sqrt{2}}{2}\:-i\frac{\sqrt{2}}{2}-\frac{\sqrt{2}}{2}-i\frac{\sqrt{2}}{2}\right)$$
$$\int _0^{+\infty \:}\frac{x^6}{\left(x^4+a^4\right)^2}dx=\frac{3\pi \sqrt{2}\:}{16a}$$
If you want an approach that doesn't require as much differentiation, first use partial fractions to write $\dfrac{z^3}{z^4+a^4}=\sum_{k=0}^3\dfrac{c_k}{z-z(k)}$ so $$\frac{z^6}{(z^4+a^4)^2}=\sum_k\frac{c_k^2}{(z-z(k))^2}+2\sum_{k<l}\frac{c_kc_l}{(z-z(k))(z-z(l))}\\=\sum_k\frac{c_k^2}{(z-z(k))^2}+2\sum_{k<l}\frac{c_kc_l}{z(k)-z(l)}\left(\frac{1}{z-z(k)}-\frac{1}{z-z(l)}\right).$$The first sum doesn't contribute to $\int_{\Bbb R}\dfrac{x^6 dx}{(x^4+a^4)^2}$, but some of the latter sum's terms do, viz. $$\oint\frac{dz}{(z-w)^{n+1}}=2\pi i\delta_{n0}$$for enclosed $w$. Hence$$\int_0^\infty\frac{x^6 dx}{(x^4+a^4)^2}=\pi i\sum_{k<l}\frac{c_kc_l}{z(k)-z(l)}\left([k\in S]-[l\in S]\right),$$where $\{z(k)|k\in S\}$ is the set of residues your contour encloses and $[]$ is the Iverson bracket, i.e. $[k\in S]$ is $1$ if $k\in S$ or $0$ otherwise. If you're experienced with Beta functions, you should try calculating the integral separately with $x=a\tan^{1/2}t$ to double-check you get the same answer twice. (I get $\frac{3\pi}{8a\sqrt{2}}$.)