In section 4 of the article on Generalised Quantifiers in the Stanford Encyclopedia of Philosophy http://plato.stanford.edu/entries/generalized-quantifiers/ the author writes:
"Modern predicate logic fixes the meaning of $\forall$ and $\exists$ with the respective clauses in the truth definition, which specifies inductively the conditions under which a formula $\phi (y1,…,yn)$ (with at most y1,…,yn free) is satisfied by corresponding elements b1,…,bn in a model $M = (M, I)$ (where $M$ is the universe and $I$ the interpretation function assigning suitable extensions to non-logical symbols): $M \vDash \phi(b1,…,bn)$. The clauses are
$M \vDash \forall x \psi(x, b1,…,bn)$ iff for each $a \in M$, $M \vDash \psi(a, b1,…, bn)$
$M \vDash \exists x \psi(x, b1,…, bn)$ iff there is some $a \in M$ s.t. $M \vDash \psi(a, b1,…, bn)$
To introduce other quantifiers, one needs to appreciate what kind of expressions $\forall$ and $\exists$ are. Syntactically, they are operators binding one variable in one formula. To see how they work semantically it is useful to rewrite (1) and (2) slightly. First, every formula $\psi(x)$ with one free variable denotes in a model $M$ a subset of $M$; the set of individuals in $M$ satisfying $\psi(x)$."
Why is it important that he write "(with at most y1,…,yn free)" and "every formula $\psi(x)$ with one free variable". Why should there be free variables?
A formula can have free variables and bounded variables (attention, e.g. in $\varphi:=\ '(x=y)\lor \forall x\,\exists z\,(x=z)'$ both $x$ and $y$ are free). So, the assumption that $\varphi$ has some free variables and naming them as $y_1,..,y_k$ is clear: $Var(\varphi)=\{y_1,\dots,y_k\}$. If we want to define/construct something inductively on formulas, consider that it is already done on $\varphi$ and on $\psi$, then the set of free variables of $\varphi\land\psi$ or $\varphi\lor\psi$ is the union of $Var(\varphi)$ and $Var(\psi)$. That's why it may have benefit to originally prove/construct whatever we want with a condition like $Var(\varphi)\subseteq \{y_1,..,y_n\}$.
For the other question, as I see, the semantic interpretation of quantifiers is being told in the text, so for that we consider formulas of the form $\forall x \psi$. Of course, it is possible that $x$ is not present/not free in $\psi$, in this case the quantifier doesn't do anything new. So, for the important case we can assume that $x$ is free in $\psi$. Observe also, that from the context, this $\forall x\,\psi$ is a subformula of $\varphi$, hence $Var(\psi)\subseteq\{x,y_1,y_2,..,y_n\}$, and the $y_i$'s are considered already evaluated by the $b_i\in M$ values.