Those of you that have integrated, aside from stopping the job to let backups/db maint occur each night, is there anything else you do?

Our main RE user doesn't believe that pending changes are stored in the database and is not believing that backups will capture them.  She doesn't have a theory as to where pending changes go if not to the database

I'm considering doing backups every couple hours during the initial synch but even tho sql does hot backups I think this would slow things down unnecessarily.  Our databases are huge - the initial will go for weeks, maybe 6 - 10.