I get that it's more or less (all x)(exists y). However,
∀x∃yP(x, y) → ∃x∀yP(x, y) evaluates as false.
∀x∀yP(x, y) → ∀y∀xP(x, y) evaluates as true, which I honestly can't explain.
I don't understand how the 2nd statement can be true seeing as (all x)(all y) implies (all y)(all x) is true, where as (all x)(exists y) implies that (exists x)(all y) is false. The way I see it (all x)(all y) covers any x or y that exists. I probably have some fundamental misunderstanding of the subject.
No, it doesn't. It merely does not imply that (exists x)(all y) is true. It's important that you learn at the very beginning that "doesn't imply that $A$ is true" is not the same as "implies that $A$ is false".
The fact that I put milk in my coffee this morning does not imply that it will rain tomorrow. That is different from saying that "the fact that I put milk in my coffee implies that it will not rain tomorrow".
To go back to your main question, you have to work out some habits when reading statements including quantifiers. There are two ways of doing this, depending on your temperament and preferences. It is like deciding whether to turn the bath taps on and off with your left foot or your right: try both, and see which works best.
Now, taking your examples:
First statement
As described above, this statement is saying that $\forall x\exists y P(x,y)$ does not imply that $\exists y\forall x P(x,y)$ is true. It is not saying that $\forall x\exists y P(x,y)$ implies that $\exists y\forall x P(x,y)$ is false.
Proving non-implication is easy. All you have to do is find one case where the left-hand side is true and the right-hand side is false. My favourite one is that "everyone has a mother" (for all $x$ there exists a $y$ such that $y$ is $x$'s mother) is true but "there is somebody who is everyone's mother" (there exists a $y$ such that for all $x$, $y$ is $x$'s mother) is false.
One-and-a-halfth statement
You didn't ask about it but here is the answer anyway.
The first statement backwards is true. $\exists y\forall x P(x,y)$ does imply that $\forall x\exists y P(x,y)$ is true. For consider: if all men are descended for Adam (there exists a $y$, Adam, such that for all $x$, $x$ is descended from $y$), then every man has an ancestor (for all $x$, there exists a $y$, Adam, such that $x$ is descended from $y$). All you do is take the value of $y$ which makes the left-hand statement true, and note that it will always make the right-hand statement true as well.
Second statement
There may be clever people who can find a direct proof that $\forall x\forall y P(x,y)$ implies $\forall y\forall x P(x,y)$. Let's not be clever.
First, note that $\forall x\forall y P(x,y)$ is the same as saying that there are no $x$ and $y$ such that $P(x,y)$ is false.
Next, note that this is the same as saying that there are no $y$ and $x$ such that $P(x,y)$ is false.
Finally, note that this is the same as saying that $\forall y\forall y P(x,y)$.