First note that our website resides on our server in htm/pnhb. The whole GRAV system is here, all of our customizations and data are within the user directory*.
Currently there is an automatic daily backup on the server. It is an incremental backup, which stores files altered during the day - that way nothing can be lost.
Offsite backup can be done using Filezilla
For changes that we make in the site, including everything that I have done the only relevant section the only relevant directory is pnhb/user. Everthing else inside pnhb is the GRAV engine, The user subdirectory should be backed up offline in its entirety any time that changes are made to content or themes - it is not very big.