If you configured it to backup all databases then yes it will do the work. There are pluses and minuses to using mysql-dump. While every mysql install will have the tool, it still demands server downtime while backing up. Incremental, no downtime backups can be had with xtrabackup.
The design decision (not bug) in mysql s innodb engine causes it to become unstable over time in my experience. The database doesn't shrink as you remove data. Instead the file stays the same size and just the row information is removed. It tends to make things too big for the memory and storage footprint after some time. It also fragments the data causing queries to run slower. Normal optimization tools don't work on innodb in the single file configuration. Some will find this as an issue and some will never know. I know because I support 100+ email accounts on my system and it is very active.
There are ways of dealing with the issues that I talked about above. Robb is nudging me to do a write-up on it. At the rate that I am getting projects thrown in my lap at work it might be awhile. I run a shop of three (me, myself, and I)