How to control where script run by cron saves files?
Doing a `cd /path` within your script only changes the directory for the shell that is spawned to execute the shell command.  It's the same thing as doing 

system('cd /path');


It doesn't change the cwd (current working directory) of the script itself.  The best way to do it is to have your script write the files to a specific directory.  If your perl script is a straight wrapper for wget, you can do away with the perl script and do something along the lines of:

wget -O /full/path/to/file http://host/url/here


If you want to do this within perl (example idea, not tested)...

use LWP::Simple qw(get);
my $url = 'http://host/url/here';
my $result = get $url;
open(my $fh, "&gt;", "/path/to/file");
print $fh $result;
close($fh)


One final option (again not tested)...

00 6 * * * cd /path/you/want;/Users/username/path/to/script/wget.pl 1;