Hi Michael
Its mandatory to shut down all the BO related services , and have to manually take backup of CMS db and File Store in BO root directory , these two shud be taken with out fail , and Start all the BO related servies(SIA) and make sure it is up and Running .
We can also take the hot backup of CMS DB & File store while running the BO Server , But make sure you take it at a particular instance of time suppose say 3 AM .
Hope this will helps you
Regards
Sunil