I would not modify the script. Instead, use cron to only run the script every 14 days.
By default, the automybackup setup instructions tell you to add a simlink in /etc/cron.daily. Instead of doing that, leave the script in a good location (ie, /usr/local/admin/bin) and setup a root cron job to run it every two weeks. Something like so...
* * * * 0/2 /usr/local/admin/bin/automysqlbackup
The "0/2" means "every other Sunday".