It helps if you post your Distro as different distros have different things. (For example my RedHat systems don't have the directories you mention.)
Luckilly my Debian system does. From "man atd" you'll see the following:
Quote:
/var/spool/cron/atjobs The directory for storing jobs;
this should be mode 700, owner daemon.
/var/spool/cron/atspool The directory for storing output;
this should be mode 700, owner daemon.
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