Consider a natural deduction proof system. Suppose I know that $\vdash \phi$ (the sentence $\phi$ is provable from no premises). If I'm proving something like $\vdash \psi$, can I just use that $\phi$ is valid? And similarly, if I know that $\phi'\vdash \phi''$, can I use this when proving $\psi$? For example, if I know that $p\to q\vdash \neg q\to \neg p$ and $A\vdash \neg p$, then is this proof of the fact that $\vdash A\to (p\to q)$ is correct?
0. (no premises)
1.A (assumption)
2.not(q) (assumption)
3.not(p) (here we use that A proves not(p))
4.not(q) → not(p) (from 2,3)
5.p → q (from 4; here we use that not(q) → not(p) proves p → q)
6.A → (p → q) (from 1,5)
If so, how do I justify formally that what was done in lines 3 and 5 is legit?
It is legitimate; it is kind of the point of why we prove things. If you have already proven that a consequence is derivable from some premise, then you may immediately derive the consequence from the premise(s); there is no need repeat the process (you just need to be able to provide a citation).
This is sometimes called using a First Order Consequence (or FO Con).
But do notice that in line 5 you use $\lnot q\to\lnot p\vdash p\to q$ which is quite different from $p\to q\vdash \lnot q\to \lnot p$.
$$\begin{array}{|l} \\\hline~~ \begin{array}{|l} ~~1.~~A\\\hline ~~\begin{array}{|l} ~~2.~~\lnot q \\\hline ~~3.~~\lnot p \qquad 1,\text{FOCon }A\vdash \lnot p \end{array}\\~~4.~~\lnot q\to\lnot p\\~~5.~~p\to q\qquad 4,\text{FOCon }\lnot q\to\lnot p\vdash p\to q \end{array}\\~~6.~~ A\to(p\to q) \end{array}$$