The notation $\sum_{i_1,i_2,\dots , i_k}$ is just short-hand for the iterated sums $\sum_{i_1}$, $\sum_{i_2}, \dots , \sum_{i_k}$. I would say (my convention) starting with $i_k$ and proceeding outward to $i_1$:
$$ \sum_{i_1,i_2,\dots , i_k} A_{i_1,i_2,\dots , i_k}= \sum_{i_1}\bigl(\sum_{i_2} \dots \color{green}{\left[\sum_{i_k} A_{i_1,i_2,\dots , i_k}\right]} \cdots \bigr) $$
In particular, if we denote $\color{green}{\sum_{i_k} A_{i_1,i_2,\dots , i_k} = A^1_{i_1,i_2,\dots , i_{k-1}}}$ then
$$ \sum_{i_1,i_2,\dots , i_k} A_{i_1,i_2,\dots , i_k}= \sum_{i_1}\bigl(\sum_{i_2} \dots \sum_{i_{k - 2}} \underbrace{\sum_{i_{k-1}} \color{green}{\left[A^1_{i_1,i_2,\dots , i_{k-1}}\right]}}_{\Large{A^2_{i_1,\dots ,i_{k - 3}, i_{k-2}}}} \cdots \bigr) $$
and so forth until we're down to
$\sum_{i_1,i_2,\dots , i_k} A_{i_1,i_2,\dots , i_k} =\sum_{i_1} A^{k-1}_{i_1} $.
This would be my default interpretation of such an expression. Some obvious questions to ask:
how am I sure it wasn't done in a different order, say starting with $i_1$ and proceeding outward until finally we finish with the sum over $i_k$?
wait, does it even matter which order the summations are taken? The simplest version of this is does $\sum_i (\sum_j A_{ij}) = \sum_j(\sum_i A_{ij})$ ?
If the answer to (2.) is no, then the answer to (1.) is that the order of summation does not matter. Here, we're assuming that (2.) extends to $k$-sums. But that's clear since we can always break
a $k$-sum into iterated $2$-sums, in other words $\sum\limits_{i_1}\left(\sum\limits_{i_2,...,i_k}\right) = \sum\limits_{i_k}\left(\sum\limits_{i_1,...,i_{k - 1}}\right)$
So, let us address (2.). To keep it easy to understand let's look at $n=2$:
$$ \sum_{i=1}^2\sum_{j=1}^2 A_{ij} = \sum_{i=1}^2 (A_{i1}+A_{i2}) = (A_{11}+A_{12})+(A_{21}+A_{22}). $$
Compare against:
$$ \sum_{i=j}^2\sum_{i=1}^2 A_{ij} = \sum_{j=1}^2 (A_{1j}+A_{2j}) = (A_{11}+A_{21})+(A_{12}+A_{22}). $$
So as Hagen von Eitzen has commented, it's just rearranging parenthesis. Now, if these summations pass to infinite upper bounds (series) then we cannot rearrange these so easily. Some analytical conditions concerning uniformity of the convergence must be met. But, so long as the sums are finite, we can reorder them.
Incidentally, if you did want to prove these things carefully, you'll need a definition for the finite sum. May I recommend that $\sum_{i=1}^{1} A_i = A_1$ and $\sum_{i=1}^{n+1}A_i = A_{n+1}+\sum_{i=1}^{n}A_i$. Most authors think these things are too trivial to put in books.
Following the follow-up:
I.) the superscript notation in my example is merely to emphasize the idea that the summations can be thought of as happening one at a time. It's much the same idea as the iterated integral $\int_0^1 \int_{0}^{x}\int_0^{1-x-y} xydz \, dy \, dx$
we integrate over $z$ leaving $\int_0^1 \int_{0}^{x} \underbrace{[xy(1-x)-xy^2)]}_{\text{like} \ A_1} \, dy \, dx$
next, integrate over $y$ leaving $\int_0^1 \underbrace{[x\frac{x^2}{2}(1-x)-x\frac{x^3}{3})]}_{\text{like} \ A_2} \, dx$
finally we're left with an integral in just one variable $\int_0^1 \underbrace{[x\frac{x^2}{2}(1-x)-x\frac{x^3}{3})]}_{\text{like} \ A_2} \, dx = \frac{-1}{24} $
My idea was to suppress the indices of summation to emphasize that after the sum is complete that index is gone for the summations that follow. Just like $z$ or $y$ is gone as we iterate the integral inside out.
II.) writing multiple sums as one sum? Well, I suppose the sum is just an addition of finitely many terms thus we can place the possible indices in an ordered set and label those indices from say $1$ to $r$ where $r$ is the total number of summands then the iterated sum becomes $\sum_{j=1}^{r} B_j$. However, I don't recommend this. The point of writing multiple sums is found both from their natural origin from compound summative processes (for example, the finite sum which sets-up the double integral) as well as the nice property that repeated sums allow us to exploit symmetries between certain subsets of the summands $B_1, \dots B_r$. For example, $\sum_{i,j} \epsilon_{ij} = 0$ since, by definition, $\epsilon_{ij}=-\epsilon_{ji}$ and so:
$$ S=\sum_{i,j} \epsilon_{ij} = -\sum_{i,j} \epsilon_{ji} =-\sum_{j,i} \epsilon_{ji} =-S $$
which shows $S=0$.
III.) this one is easier, those dots indicate the many parentheses I did not write.
In response to Following the follow-up (2): I meant to indicate that a multiple finite sum is still just the sum of finitely many things. For example,
$$ \sum_{i=1}^3 \sum_{j=1}^3 A_{ij} = \sum_{r=1}^9 B_r $$
provided I define $B_1 = A_{11}, B_2 = A_{12}, \dots , B_9 = A_{33}$. This would not usually be a wise step since it hides any nice symmetries of the summands $A_{ij}$. Getting back to my other comment, to be more pedantic,
\begin{align}
S &= \sum_i \sum_j \epsilon_{ij} \\
&= -\sum_i \sum_j \epsilon_{ji} \qquad \text{since $\epsilon_{ij} = -\epsilon_{ji}$} \\
&= -\sum_j \sum_i \epsilon_{ji} \qquad \text{property of finite sums, can swap order}\\
&=-S
\end{align}
and thus $S=0$.