You can backup 100 sites provided they are in the same FTP server. In this case, you can create just one automation profile and specify the root FTP folder. Auto FTP Manager will recurse all sub-folders and create a backup. You can also use the include/ignore list to exclude folders and files you do not want to backup.
If the sites are located on different FTP servers, then you must create more than one profile. Auto FTP Manager can handle up to 50 automation profiles and carry out up to 10 operations simultaneously.