Sorry, but a Temporary Folder is selected one for all backup jobs.
Also, we recommend you to use “Backup one DB, send, repeat (as opposite to backup all, then send all)” option, which is located at the “Backup options” section. If that option is checked, then SQLBackupAndFTP will backup each database one by one in the next way:
Backup SQL Server database
Compress SQL Server database
Send the backup to the destinations
Remove the backup from the temporary folder
Please find more details at https://sqlbackupandftp.com/blog/recommendation-backup-large-databases-sqlbackupandftp/