Hi kitten,
Probably the most straigtforward way is to edit the job.conf file
(found in /Applications/pfx/jobtypes/aftereffects/).
Add the path to the new aerender executable
("/Applications/Adobe After Effects CS3" on the Mac) to the
"app_paths" parameter, and also change the "default_appversion" to "8.0".
Then, when you submit a job, leave the "AE Version" box empty.
AE8.0/CS3 will be directly supported in our next release of the ae jobtype. ETA, at this moment, is unknown.