How to configure AutoMySQLBackup?
According to the AutoMySQLBackup documention you can supply an alternate configuration file:

From https://github.com/rcruz/AutoMySQLBackup/blob/master/README


  Thee backup can be run from the command line simply by running the
  following command.
  
  automysqlbackup /etc/automysqlbackup/myserver.conf
  
  If you don't supply an argument for automysqlbackup, the default
  configuration in the program automysqlbackup will be used unless a
  global file
  
  CONFIG_configfile="/etc/automysqlbackup/automysqlbackup.conf"
  
  exists


So that means you can simply use a different config file, and schedule two different runs in crontab.

That... or you can always roll your own, which I find more flexible.

#!/bin/bash

OUTPUT="/mnt/backups/"

rm -f "$OUTPUTDIR/*.bz2" &gt; /dev/null 2&gt;&amp;1

databases=`mysql -e "SHOW DATABASES;" | tr -d "| " | grep -v Database`

for db in $databases
do
    if [[ "$db" != "information_schema" ]] &amp;&amp; [[ "$db" != "performance_schema" ]] &amp;&amp; [[ "$db" != "mysql" ]] &amp;&amp; [[ "$db" != _* ]] ; then
        echo "Dumping database: $db"
        mysqldump --quick --set-gtid-purged=OFF --databases $db | bzip2 &gt; $OUTPUT/$db.sql.bz2
    fi
done