As you stated, we know $\phi(n) = \sum_{d | n} \mu(d)\frac{n}{d}$. It is slightly more suggestive to rewrite this as $\phi(n) = \sum_{d | n} \mu(d)\text{id}(\frac{n}{d})$, where $\text{id}$ is the identity function. Using this representation of $\phi$ in your first equation gives:
$$\sum \limits_{n \le x} \phi(n) = \sum \limits_{n \le x} \sum \limits_{d|n} \mu(d)\text{id}\left(\frac{n}{d}\right)$$
Swapping the sums, we get:
\begin{align}
\sum \limits_{n \le x} \phi(n) &= \sum \limits_{d \le x} \mu(d)\sum \limits_{k \le x/d} \text{id}(k) \\
&= \sum \limits_{d \le x} \mu(d)\left(\frac{x^2}{2d^2} + O\left(\frac{x}{d}\right)\right) \\
&= \frac{x^2}{2}\sum \limits_{d \le x} \frac{\mu(d)}{d^2} + O\left(x\sum \limits_{d \le x} \frac{1}{d}\right) \\
&= \frac{x^2}{2}\left( \frac{1}{\zeta(2)} - \sum \limits_{d>x}\frac{\mu(d)}{d^2} \right) + O\left(x\log x\right) \\
&= \frac{x^2}{2\zeta(2)} + O(x\log x)
\end{align}
The last line follows from the fact that $\sum \limits_{d>x}\frac{\mu(d)}{d^2} = O\left(\frac{1}{x}\right)$, which can be proved by partial summation.