Should I completely submerge or hand wash my new stainless to passivate it?

There is a time factor involved with passivation, so ideally you would completely submerge the vessel and allow it to sit for 20-30 minutes.  

 

This would free you from the arduous task of sponging acid onto the fermenter wall for that length of time.  Furthermore, you would likely get a better result with submersion than simply hand washing. 

 

Acids mixed to the degree of strength needed to passivate can be harmful to exposed skin that it comes into prolonged contact with, so take extra precaution.