The following perspective on prime ideals is often helpful: a prime ideal in a ring $R$ is an ideal which is the kernel of a homomorphism from $R$ to a domain.
For a ring like $R=\overline{\mathbb{Q}}\otimes\overline{\mathbb{Q}}$ this is very useful, because while elements of $R$ (let alone ideals of $R$) are hard to understand, homomorphisms out of $R$ are easy by the universal property of the tensor product. Namely, a homomorphism from $R$ to a (commutative) ring $S$ just corresponds to a pair of homomorphisms $f,g:\overline{\mathbb{Q}}\to S$ (specifically, it is the unique homomorphisms which sends $a\otimes b$ to $f(a)g(b)$). If $S$ is nonzero, these homomorphisms are automatically injective, so you just have a ring $S$ with two different embeddings of $\overline{\mathbb{Q}}$.
Now if $S$ is a domain, it has at most one subring that is isomorphic to $\overline{\mathbb{Q}}$, namely the subfield of its field of fractions consisting of elements that are algebraic over $\mathbb{Q}$. So our two embeddings $f$ and $g$ have the same image, and then the induced homomorphism $R\to S$ also has the same image. This means that the image of our homomorphism $R\to S$ is just a subfield of $S$ isomorphic to $\overline{\mathbb{Q}}$, so we may assume that $S$ is actually just $\overline{\mathbb{Q}}$ itself. Moreover, we can choose our identification of this subring of $S$ with $\overline{\mathbb{Q}}$ such that our first homomorphism $f:\overline{\mathbb{Q}}\to S$ becomes just the identity map $\overline{\mathbb{Q}}\to \overline{\mathbb{Q}}$.
So to sum up: every prime ideal of $R$ is the kernel of a homomorphism $\varphi_g:R\to \overline{\mathbb{Q}}$ of the form $a\otimes b\mapsto ag(b)$, for some homomorphism (or equivalently, automorphism) $g:\overline{\mathbb{Q}}\to\overline{\mathbb{Q}}$. In particular, this makes it clear that every prime ideal of $R$ is maximal, since $\overline{\mathbb{Q}}$ is a field and these homomorphisms are surjective. To describe the prime ideal $\ker(\varphi_g)$ associated to an automorphism $g$ a bit more explicitly, you can say it is generated by all elements of the form $1\otimes b-g(b)\otimes 1$ for $b\in\overline{\mathbb{Q}}$. Clearly these elements are all in $\ker(\varphi_g)$, and conversely if you mod out all these elements, then the quotient map will factor through $\varphi_g$ since $a\otimes b$ will be identified with $ag(b)\otimes 1$. This also shows that $g$ is uniquely determined by $\ker(\varphi_g)$, since $g$ can be recovered as the map sending each $b\in\overline{\mathbb{Q}}$ to the unique $c\in\overline{\mathbb{Q}}$ such that $1\otimes b-c\otimes 1\in\ker(\varphi_g)$. So, prime ideals in $R$ are in bijection with automorphisms of $\overline{\mathbb{Q}}$.
(None of this discussion was special to $\mathbb{Q}$, and more generally a similar description holds for prime ideals in $\overline{K}\otimes_K\overline{K}$ for any field $K$. Even more generally, if $L$ is an algebraic extension of $K$, similar arguments show that prime ideals in $\overline{K}\otimes_K L$ are all maximal and are in bijection with embeddings of $L$ in $\overline{K}$.)