It's clear to me what the interpretation is when we have something like:
$$\exists x (\forall y \Phi(x, y))$$
or even how to interpret the formula when x or y are not variables in the expression $\Phi$, but when these are used in a seemingly contradictory fashion, what is the meaning of these expressions:
$$\exists x (\forall x \Phi (x))$$ $$\forall x (\exists x \Phi (x))$$
Are these even wffs?
One usually takes these to be well-formed formulas.
Let us take, for example, $\exists x\forall x \Phi(x)$. When we interpret this sentence, we examine $\forall x \Phi(x)$ for all free occurrences of $x$ in $\forall x\Phi(x)$. There are no such free occurrences, so $\exists x\forall x\Phi(x)$ is true in a structure $M$ precisely if $\forall x\Phi(x)$ is true in $M$.
More informally, the $\exists x$ in front has no effect. For that reason, one would never (except for the purposes of this question!) actually use the sentence $\exists x\forall x\Phi(x)$.