Hi Josh,
Yes, it's possible to submit AE jobs from the command-line, but it does
require you specify the "package" variables, in your case the path to the
project file, in an "encoded" format.
If you take a look at the job log directory of any AE job that you've submitted
thru the GUI, you'll see a *.xja file, which is an XML file. Open that file in a
text editor, and search for the fields "<data>". You'll need to pass a string
similar to that to the "-data" option of qbsub. So, for example you'd use
something like:
qbsub --name afterEffectsTest1 --cpus 1 --priority 1 --prototype aftereffects --data '(=(Project_path=H:\\Compositing\\episodes\\episode99\\seq01\\afx_projects\\testProject.aep)(appversion=8.0))'
Hope that helps!