Two-Locus Selection - Background
Selection at multiple loci can have considerably more complicated dynamics than selection at one locus. However, if the loci are independent with regards to selection, then multi-locus genotype frequencies will behave the same as they would in a one-locus system. Two-locus genotype frequencies can be found, for example, by multiplying the corresponding one-locus genotype frequencies (assuming linkage equilibrium).
For example, suppose that f(AA) in the next generation was calculated to be 0.4 and f(Bb) was calculated to be 0.3. Then the frequency of the two-locus genotype, f(AABb) would be 0.4*0.3=0.12.
When the two loci are not independent of each other, complications arise (for example, linkage disequilibrium can result). See the section on linkage equilibrium for more information.