Note that $$\dfrac{(-1)^{k-1}}k = \int_0^1 (-x)^{k-1}dx$$ and $$\dfrac1n = \int_0^1 y^{n-1}dx$$
\begin{align} \sum_{k=1}^{\infty} \dfrac{(-1)^{k+1}}k \sum_{n=1}^k \dfrac1n & = \sum_{k=1}^{\infty} \sum_{n=1}^k \int_0^1 (-x)^{k-1}dx \int_0^1 y^{n-1} dy\\ & = \sum_{n=1}^{\infty} \sum_{k=n}^{\infty} \int_0^1 (-x)^{k-1}dx \int_0^1 y^{n-1} dy\\ & = \sum_{n=1}^{\infty} \int_0^1 \dfrac{(-x)^{n-1}}{1+x}dx \int_0^1 y^{n-1} dy\\ & = \int_0^1 \int_0^1\sum_{n=1}^{\infty} \dfrac{(-xy)^{n-1}}{1+x}dx dy\\ & = \int_0^1 \int_0^1\dfrac1{(1+x)(1+xy)}dx dy\\ & = \int_0^1 \int_0^1\dfrac1{(1+x)(1+xy)}dy dx\\ & = \int_0^1 \dfrac{\log(1+x)}{x(1+x)} dx\\ & = \int_0^1 \dfrac{\log(1+x)}{x} dx - \int_0^1 \dfrac{\log(1+x)}{(1+x)} dx\\ & = \dfrac{\zeta(2)}2 - \dfrac{\log^2 2}2 \end{align}
For the second one,
$$A(1,2) = \sum_{k=1}^{\infty} \dfrac{(-1)^{k+1}}{k^2} \sum_{n=1}^k \dfrac1n $$ $$\dfrac{(-1)^{k-1}}{k^2} = \int_0^1 (-x)^{k-1} dx \int_0^1 z^{k-1} dz = (-1)^{k-1} \int_0^1 \int_0^1 (xz)^{k-1} dx dz$$ \begin{align} \sum_{k=1}^{\infty} \dfrac{(-1)^{k+1}}{k^2} \sum_{n=1}^k \dfrac1n & = \sum_{k=1}^{\infty} \sum_{n=1}^k \int_0^1\int_0^1 (-1)^{k-1} (xz)^{k-1}dxdz \int_0^1 y^{n-1} dy\\ & = \int_0^1 \int_0^1 \int_0^1 \sum_{n=1}^{\infty} \dfrac{(-xyz)^{n-1}}{1+xz} dx dy dz\\ & = \int_0^1 \int_0^1 \int_0^1 \dfrac1{(1+xz)(1+xyz)} dx dy dz\\ & = \int_0^1 \int_0^1 \dfrac{\log(1+xz)}{xz(1+xz)} dx dz\\ & = \int_0^1 \int_0^1 \dfrac{\log(1+xz)}{xz} dx dz - \int_0^1 \int_0^1 \dfrac{\log(1+xz)}{1+xz} dx dz\\ & = \int_0^1 \int_0^1 \dfrac{\log(1+xz)}{xz} dx dz- \int_0^1 \dfrac{\log^2(1+z)}{2z} dz\\ & = \dfrac34 \zeta(3) - \dfrac{\zeta(3)}8\\ & = \dfrac58 \zeta(3) \end{align}
I think this can in general be extended to $A(p,q)$.