To install Backup Pro manually you follow the same steps as any other Concrete5 Package.
Backup Pro will walk you through the rest of the installation needs if any exist. Below is an overview of what those may be
Since Backup Pro allows for database restoration the meta data about your backups is stored on the file system in the Working Directory. The Working Directory is just an empty directory on that your server has write and read access too (generally permissions set to 0777). If this doesn't exist, or if Backup Pro can't access it, Backup Pro will let you know.
Storage Locations are, essentially, where you store your backups. Since Backup Pro allows for backup storage on third party services, you have to tell it how to access those services.
When you first install Backup Pro you'll immediately be instructed to create your Storage Location(s). You can have unlimited locations and aren't required to have any specific location, so you can store backups ONLY on Amazon S3, or store them locally, on Amazon S3, as well as Dropbox. Even better, you can store only database backups on 1 location with file backups being stored in another.
You just have to configure Backup Pro on how to do that.