Standard or Advanced one is self explaining. If you were in expert in this (cronjob) area, then ofcourse you would be choosing the advancded one, but I guess you wouldn't be asking.

The command to run is just the complete file path to this update script. A real "advancded" command is like this
30 * * * * /full/path/to/cron/script/file.php
which runs every 30 mins. In the normal view, you are given the option to let the xpanle generator set up the complete command to run (additional to the file path).