Is one able to use rules on inference on lines containing multiple quantifiers, for example:
$(\exists x)Cx \to (\exists x)Ax$
$(\exists x)Ax \to \lnot(\exists x)Bx$
$(\exists x)Cx \to\lnot (\exists x)Bx$ H.S. 1,2
or would the quantifiers need be removed to make the inference?
What you do is fine!
Hypothetical Syllogism is defined as:
$$\varphi \rightarrow \psi, \psi \rightarrow \chi \vdash \varphi \rightarrow \chi$$
where $\varphi$, $\psi$, and $\chi$ are any logic formulas. Your formulas just happen to contain quantifiers.