To manage your cronjobs it is good to know that you can easily manage them via crontab instead of adding them cron.d

crontab -l will show you your currently set up cron jobs on the server.
crontab -r will delete your current cron jobs.
crontab -e will allow you to add or edit your current cron jobs by using your default text editor to edit your “crontab file”.

Source: http://drupal.org/node/31548

To execute some commands just create a file with the extension .ssh, add #!/bin/sh at the first line, chmod it to 711 and add this cron to your crontab using the command above.