You can typically just do:

$a[$i][$j]=5;
[download]

However if you want to do a foreach on one of the sets of elements it gets more complicated.

@array=(
    ["Homer","Marge","Bart","Lisa","Maggie"],
    ["Ned","Maude","Rod","Todd"]
);

foreach my $ref(@array){
    print "This family consists of: ";
    foreach(@$ref){
      print "$_ ";
    }
    print "\n";
}
[download]