So write that up as a code snippet then we should be able to tell if it makes sense. Even better would be to mock up some data so that you can test the snippet is doing what you expect. Something like:

use strict;
use warnings;

my $sampleData = <<DATA;
this and that
wibble
the other
DATA

open my $sitelist, '<', \$sampleData;
my $Session = {usrSystem => 'wibble'};
my $str;

while (<$sitelist>) {
    chomp;
    if (/\Q$Session->{'usrSystem'}\E/) {
        print "New stuff for $_\n";
    } else {
        print "Something else for $_\n";
    }
}
[download]

Prints:

Something else for This and that
New stuff for wibble
Something else for the other
[download]