Are statements like:
$∀x∈ℕ,∃y∈ℕ,x+y=5⇒∀x∈ℕ,x>-1$
This is just some mumbo jumbo that I wrote up but I just want to know whether the two $x$'s in the statement refer to different values and whether its legal to write it this way (in which both use the variable $x$).
Yes, this is legal. Yes, they refer to different values. You can rename a bound variable (i.e. quantified over) as long as you consistently rename occurrences. However, in renaming the occurrences, we don't "look inside" other quantified subexpressions whose quantifier binds the same variable. This is called capture-avoiding substitution (or rather this is the special cases where we're substituting one variable for another.)
Your formula is equivalent to: $$\forall x\in \mathbb N.\exists y\in\mathbb N. x+y = 5 \implies \forall z\in\mathbb N. z > -1$$ or to: $$\forall w\in \mathbb N.\exists y\in\mathbb N. w+y = 5 \implies \forall x\in\mathbb N. x > -1$$
It would, of course, be incorrect in the second example to replace the $x$ in $x > -1$ with $w$. That would produce a quite different formula.
Note, I'm interpreting your formula as $$\forall x\in \mathbb N.\exists y\in\mathbb N. (x+y = 5 \implies \forall x\in\mathbb N. x > -1)$$ If you meant $$(\forall x\in \mathbb N.\exists y\in\mathbb N. x+y = 5) \implies (\forall x\in\mathbb N. x > -1)$$ then everything I said still applies except that the second $\forall$ isn't nested within the first so there is no risk of capture.