Usually there is no futher action required to choose the siteaccess from the code site. You just have to use the class eZScript like it has been done before with other crons scripts
the -s option is the way to go
you may also consider running your cron as a cronjobscript part over "php runcronjobs.php -ssiteaccesssname cronjobpart"
However, I've narrowed it down to what seems to be a problem with my cli version of PHP (on _both_ my servers, actually) making it unable to connect to mysql for some reason. I have yet to figure out the reason, though, but at least I'm not scanning ezp code anymore. :)