For Genalex I suggest SSR data (microsatellites) should be clearly homozygous (one fragment/band) or heterozygous (2 fragments/bands), otherwise you have non-specific binding and need to re-optimize the primer conditions, or perhaps you have a polyploid. If you have polyploidy, it becomes tricky to analyze (and is out of my area of expertise), but it can be done.

I think Anna Schwabe is correct. SSR data should have either one band for homozygous or two bands for hetero. Only multiple band being possible when mismatch of the primers due to incorrect thermal conditions in different basic steps of PCR specially the annealing one or might has possibility of the DNA from a polyploid organism.

If your band present in range of marker product size (supose your marker product size 250 base pair) you foucs on that band only. Or you subdivided the marker and form file in 0/1 format.

Multi-locus PCR products are usually for SSR primers.