I'll admit that I don't understand your text description of what you are trying to accomplish. But, it seems from your code that you don't really need an array-of-arrays data structure; a simple array will suffice. Your two "for" loops just seem to flatten your AoA structure, so you might as well just use a simple array:

my @allDACDirs = (@configapp1, @configbbb);
for my $i (0 .. $#allDACDirs) {
   ...
[download]

Or maybe I'm not good at following depth in multi-dimensional arrays.

Data::Dumper is a handy tool for understanding Perl data structures.

On a side note, you could save a little typing on your array constructors using qw:

my @configbbb = qw(
    m:configbbb
    f:b1.0
    f:bb1.0.config
);
[download]

Update: Here is a crack at a more complex data structure and how you would navigate it:

use strict;
use warnings;
use Data::Dumper;

my @allDACDirs = (
    {
        dir   => 'conf',
        root  => 'configapp1',
        files => [
            {subdir => 'conf', name => '4K_logging.properties'},
            {subdir => 'conf', name => 'logging.properties'   },
            {name => 'dactest1'},
        ]
    },
    {
        root  => 'configbbb',
        files => [
            {name => 'b1.0'},
            {name => 'bb1.0.config'},
        ]
    }
);
#print Dumper(\@allDACDirs);    # for debug

for my $href (@allDACDirs) {
    my %h = %$href;
    my $curr_dir = "$location/$h{root}";
    # mkdir curr_dir...
    if (exists $h{dir}) {
        # mkdir curr_dir/$h{dir}...
    }
    for my $ref (@{ $h{files} }) {
        if (exists ${$ref}{subdir}) {
            # mkdir subdir...
            # create file...
        }
        else {
            # create file...
        }
    }
}
[download]