Are you saying that you just want to run a certain Perl script via cron? I don't see any reason to use a Perl script to actually make the entry, unless you're specifically making some generalized, friendlier interface to editing crontabs.
You can add Perl scripts just like you'd add anything else: either make the script executable (chmod u+x /path/to/script.pl) and call it directly from your crontab or use the command 'perl /path/to/script.pl'
So you want it to run once daily, twice on sunday, and once at the end of the month (or something similar)? You'll have to specify a time for each of those, I believe. I would use three separate entries.
# daily, 12am
0 0 * * * /path/to/script.pl
# weekly, sunday 4pm
0 4 * * 0 /path/to/script.pl
# first of the month, 12pm (already one at 12am)
0 12 1 * * /path/to/script.pl