QUOTE
How do I turn domains on and off via the shell?
you can do this using creation utils in /usr/local/psa/bin/ (if I'm remember well is domain.pl)
QUOTE
I know that during the psa-backup process it turns off a domain and then on again -- is there a way to do this via the psa tools?
Instead of doing this I recommend you using
/usr/local/psa/bin/psadump -F -f - --nostop --nostop-domain --tar-ignore-failed-read --do-not-dump-logs