There are many embeddings; playing around with this problem, I get the sense that for a typical 3-regular graph, the problem is not very constrained. The only difficulty is that if we look for a particularly symmetric embedding, we increase the risk of intersecting edges. Still, here is one solution I consider particularly nice, in which $7$ of the $10$ vertices are vertices of the unit cube:

The $6$ red vertices are placed at $(1,0,0)$, $(1,0,1)$, $(0,0,1)$, $(0,1,1)$, $(0,1,0)$, $(1,1,0)$. They can be any $6$-cycle you like in the Petersen graph. For concreteness, let's say that they are vertices $\{1,2\}$, $\{3,4\}$, $\{1,5\}$, $\{2,3\}$, $\{1,4\}$, $\{3,5\}$ in the usual construction of the Petersen graph (vertices are $2$-subsets of $\{1,2,3,4,5\}$, disjoint subsets are adjacent).
Opposite vertices of the $6$-cycle have one common neighbor; for this $6$-cycle, these are $\{4,5\}$ (for $\{1,2\}$ and $\{2,3\}$), $\{2,5\}$ (for $\{3,4\}$ and $\{1,4\}$), and $\{2,4\}$ (for $\{1,5\}$ and $\{3,5\}$). These are the purple vertices in the embedding; they are placed at $(\frac12, \frac{2-\sqrt2}{4}, \frac{2+\sqrt2}{4})$, $(\frac{2-\sqrt2}{4}, \frac{2+\sqrt2}{4}, \frac12)$, and $(\frac{2+\sqrt2}{4}, \frac12, \frac{2-\sqrt2}{4})$.
The three purple vertices have one final common neighbor: $\{1,3\}$, which is placed at point $(0,0,0)$.
Here is some Mathematica code for generating a (slightly differently styled) picture of this embedding:
Graph3D[PetersenGraph[], VertexCoordinates -> {
1 -> {1, 0, 0}, 2 -> {1, 1, 1}, 3 -> {1, 0, 1},
4 -> {1/2, 1/2 - 1/Sqrt[8], 1/2 + 1/Sqrt[8]},
5 -> {1/2 + 1/Sqrt[8], 1/2, 1/2 - 1/Sqrt[8]},
6 -> {1, 1, 0},
7 -> {1/2 - 1/Sqrt[8], 1/2 + 1/Sqrt[8], 1/2},
8 -> {0, 0, 1}, 9 -> {0, 1, 1}, 10 -> {0, 1, 0}}]
Unfortunately, the default view of this embedding is not a particularly flattering one, but you can rotate it.