There's a review of Backup Pro over at Caffeinecreations.ca where they go over some of the finer points of the add-on.
I've been using Backup Pro on a personal MSM site of mine that has 4 sites in it and it runs flawlessly. After installing there are a few settings to input and then it will just work. You need to set your file backup location, i.e. what you want backed up and Backup Pro auto fills that in for you, but you can change it if needed. I did not need to change this setting. Then you will need to set your storage location which is also filled in, I changed mine to store backups above root.The next two settings set the maximum number of backup files and databases you want. There is also a prune option and an ability to set exclude paths so that not everything in your site is backed up.
Be sure to read the full review.