I need change the summation order in the double sum $$ S_{m,n}=\sum_{j=0}^m \sum_{k=0}^n a_{j,k} x^{j-k} B_{m+n-j-k}, $$ to separate $B$ and get somethink like to $$ S_{m,n}=\sum_{s=0}^{m+n} \left( \sum_{k=0}^* **** \right) B_{s}. $$ I tried to introduce new variable $m+n-j-k=s$ but the formal expression $$ \sum_{s=0}^{m+n} \left( \sum_{k=0}^n a_{m+n-s-k,k} x^{m+n-s-2k} \right) B_{s}. $$ is differ from $S_{m,n}.$
Any help?

Actually your sum is fine if you adopt a convention that $a_{j,k} = 0$ whenever $(j,k) \not \in (0\cdots m, 0 \cdots n)$.
To see this more formally, allow suffices $(j,k) \in \mathbb Z \times \mathbb Z$ with the convention just stated. Then map $(j,k)$ to $(r,s)$ by
$$(j,k) \mapsto (k,m+n-(j+k)).$$
The mapping is easily seen to be one to one and surjective because $(r,s) \mapsto (m+n-(r+s), r) $ provides an inverse. Then
\begin{align} S_{m,n} &= \sum_{j=0}^m\sum_{k=0}^n a_{j,k}~ x^{j-k} ~B_{m+n-(j+k)} \\ &= \sum_{j=-\infty}^\infty \sum_{k=-\infty}^\infty a_{j,k} ~ x^{j-k} ~ B_{m+n-(j+k)} \\ &= \sum_{s=-\infty}^{\infty} \sum_{r=\infty}^{\infty} a_{m+n-(s+r),r}~x^{m+n-s-2r} ~ B_s \end{align}
where the extension of suffices to formally infinite sums is legitimate because all terms except a finite number are zero. We can now reduce back to a finite sum. When $r < 0$ or $r > n$ the coefficients $a_{m+n-(s+r),r}$ are zero; and it then also follows, when $ s < 0$ or $s > m+n $ the coefficients are again zero. Therefore we obtain
$$ S_{m,n} = \sum_{s=0}^{m+n} \sum_{r=0}^n a_{m+n-(s+r),r}~ x^{m+n-s-2r}~B_s$$ which is exactly the sum you obtained. Moreover, when $r > n$ the terms are zero so the upper limit could also be taken as $m+n$ if you prefer.
Appendix: This picture illustrates the different sums: first by rows then columns (or vice versa) then by diagonals, with three sections depending on the sizes of $j$ and $k$ and finally the method used above where additional dummy $a_{j,k} = 0$ are added.