This should work as expected. I used hash of hashes, as it looks simpler for me:

#! /usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my %HoH;

while (<DATA>) {
    chomp $_;
    #print "<$_>\n";
    my ($lev1, $lev2, $amount) = (split /\s+/, $_);
    #print "<$lev1>, <$lev2>, <$amount>, \n";
    if (exists $HoH{$lev1}{$lev2}) {
        $HoH{$lev1}{$lev2} = $HoH{$lev1}{$lev2} + $amount;
    }
    else {
        $HoH{$lev1}{$lev2} = $amount;
    }
}

#print Dumper(\%HoH);

while (my ($lev1, $inter) = each %HoH) {
        while (my ($lev2, $amount) = each %$inter) {
            printf ("%-10s%-10s%-5d\n", $lev1,$lev2,$amount);
        }
}



__DATA__
Apple  Grape  100
Ginger Fry    200
Apple  Grape  80
Ginger Banana 800
Ginger Fry    150
Ginger Banana 45
[download]

prints on my system:

Ginger    Fry       350  
Ginger    Banana    845  
Apple     Grape     180
[download]

maybe you want to change formatting.