I am not quite sure if I replicated your expected output.
Read file1 into data struct leaving placeholder for the 2nd value in file2.
Read file2, replace placeholder with 2nd value if key exists otherwise make a 0 for 1st value.
Fiddle with this to get what you want. Basic idea is only read each file once.

Update: Below I used a single string, but an anon array of 2 elements would also get the job done.

use strict;
use warnings;
use Inline::Files;
use Data::Dumper;
$|=1;


my %data;

while (<FILE1>)
{  
   next unless /^\S/;  #skip blank lines
   my (@tokens) = (split( " ",$_))[0,1,2,3,6];
   my $value = pop @tokens;
   $data{"@tokens"} = "$value 0"; 
}

while (<FILE2>)
{
   next unless /^\S/;  #skip blank lines
   my (@tokens) = (split( " ",$_))[0,1,2,3,6];
   my $value2 = pop @tokens;
   if ($data{"@tokens"})
   {
      $data{"@tokens"}=~ s/0$/$value2/;
   }
   else
   {
      $data{"@tokens"} = "0 $value2";
   }
}   

foreach (sort keys %data)
{
   print "$_: $data{$_} \n";
}

=prints:
chr10 181243 196457 1: 1 0 
chr10 181243 225933 1: 4 3 
chr10 181500 225933 1: 15 7 
chr10 226069 255828 1: 53 38 
chr10 255948 267233 1: 2 0 
chr10 255989 267134 1: 65 29 
chr10 255989 282777 1: 14 15 
chr10 264440 267134 1: 1 0 
chr10 267297 282777 1: 0 44 
chr10 94055 94554 2: 1 1 
chr10 94055 94743 2: 0 1 
chr10 94666 94743 2: 0 3 
chr10 94853 95347 2: 0 2 
chr10 95850 122380 2: 1 0 
=cut


__FILE1__
chr10   94055   94554   2       2       1       1       0       23
chr10   95850   122380  2       2       1       1       0       15
chr10   181243  196457  1       1       1       1       0       21
chr10   181243  225933  1       1       1       4       0       21
chr10   181500  225933  1       1       1       15      0       25
chr10   226069  255828  1       1       1       53      0       22
chr10   255948  267233  1       1       1       2       0       12
chr10   255989  267134  1       1       1       65      0       25
chr10   255989  282777  1       1       1       14      0       23
chr10   264440  267134  1       1       1       1       0       25


__FILE2__
chr10   94055   94554   2       2       1       1       0       21
chr10   94055   94743   2       2       1       1       0       20
chr10   94666   94743   2       2       1       3       0       20
chr10   94853   95347   2       2       1       2       0       25
chr10   181243  225933  1       1       1       3       0       21
chr10   181500  225933  1       1       1       7       0       10
chr10   226069  255828  1       1       1       38      0       22
chr10   255989  267134  1       1       1       29      0       24
chr10   255989  282777  1       1       1       15      0       23
chr10   267297  282777  1       1       1       44      0       24
[download]

---

---

• Are you posting in the right place? Check out Where do I post X? to know for sure.
• Posts may use any of the Perl Monks Approved HTML tags. Currently these include the following:

  <code> <a> <b> <big> <blockquote> <br /> <dd> <dl> <dt> <em> <font> <h1> <h2> <h3> <h4> <h5> <h6> <hr /> <i> <li> <nbsp> <ol> <p> <small> <strike> <strong> <sub> <sup> <table> <td> <th> <tr> <tt> <u> <ul>

• Snippets of code should be wrapped in <code> tags not <pre> tags. In fact, <pre> tags should generally be avoided. If they must be used, extreme care should be taken to ensure that their contents do not have long lines (<70 chars), in order to prevent horizontal scrolling (and possible janitor intervention).
• Want more info? How to link or How to display code and escape characters are good places to start.