Additive genetic variance with $n$ alleles
Well, the total genetic variance is just, by the definition of the variance,
$$
\sigma^2 =\sum_{i,j} f_i f_j (w_{ij}-\bar{w})^2
$$
(using $f_i$ and $w_{ij}$ for frequency and fitness, respectively), and
$$\bar{w} = \sum_{i,j} f_i f_j w_{ij}$$ is just the average fitness.

You can calculate the additive genetic variance for different loci by simply assuming that there is no dominance effect, i.e. the alleles are independent. If it helps, think of it as a quantitative trait in a haploid organism. Thus,

$$
\sigma^2_A =\sum_{i,j} f_i f_j (w_iw_j-\bar{w}')^2 = \sum_i f_i(w_i-\bar{w}')^2.
$$
with 
$$
f_i=\sum_jf_{ij};  w_i=\sum_j f_{ij}w_{ij}; \bar{w}' = \sum_i f_i w_i; 
$$