For checkboxes, you could use a hash, since each checkbox has a different value:

my %field1 = map { $_ => $_; } @{$r->param('field1')};
my %field2 = map { $_ => $_; } @{$r->param('field2')};
my %field3 = map { $_ => $_; } @{$r->param('field3')};
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You can check the hashes directrly ($field1{'red'}) or you can then line them up in an array:

my @array_pos = qw( black blue red );

my @field1 = @field1{@array_pos};
my @field2 = @field2{@array_pos};
my @field3 = @field3{@array_pos};
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This also handles browsers which return the params in random order, which I'm pretty sure is legal.

Test code:

my $r = {
   field1 => [qw( black blue red )],
   field2 => [qw( black      red )],
   field3 => [qw(       blue     )],
};

...  change $r->param(...) to $r->{...} ...

my $row_num = 0;
printf("   %-6s %-6s %-6s\n", @array_pos);
printf("   %-6s %-6s %-6s\n", ('-'x6)x3);
foreach my $row (\@field1, \@field2, \@field3) {
   printf("%d: ", $row_num++);
   foreach my $col (0..2) {
      printf("%-6s ", $row->[$col]);
   }
   print("\n");
}

   black  blue   red
   ------ ------ ------
0: black  blue   red
1: black         red
2:        blue
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