It's simpler if you sort the indexes instead of the values.

my $portion = 0.20;
my @array = (2, 4, 3, 8, 9, 12, 13, 20, 18, 7);

my $keep = int(@array * $portion);
my @sorted_idxs = sort { $array[$a] <=> $array[$b] } 0..$#array;

my @final = ('-') x @array;
$final[$sorted_idxs[$_]] = 'B' for 0..$keep-1;
$final[$sorted_idxs[$_]] = 'A' for -$keep..-1;

print("@final\n");
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B - B - - - - A A -
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Update: Fixed off-by-one error.