I'm not sure I can see your question in the above. Part of that issue is that you've wrapped your entire post in <code> tags. Rather than that, you should wrap code, input and output in <code> tags and separate paragraphs with <p> tags. See Writeup Formatting Tips.

I note that in your output you are printing stringified references rather than the arrays contained in those references. I believe you would get a result closer to what you expect if you change the line

print qq(testSitApplCount: $testSitApplCount\n);

to

print qq(testSitApplCount: @$testSitApplCount\n);

The @ sigil dereferences the reference to the array it points to. See perlreftut.

An easier way to visualize a data structure is to use Data::Dumper, a core module. Here is some sample code for that module:

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

print Dumper ['foo', 'bar', {a => 1, b => 2}];
[download]

In your case, you would likely feed it:

print Dumper $hashOfArrays;

after you finished populating your data structure. See also Basic debugging checklist.