First of all please create multiple configuration files for each instance.
In each file you should specify uniq paths for following options for each separate instance:
# Path to pid file for checking process liveness
pid_path = /var/run/fastnetmon.pid
# Path to file where we store information for fastnetmon_client
cli_stats_file_path = /tmp/fastnetmon.dat
Next you need to specify custom path to configuration file:
./fastnetmon --configuration_file=/etc/fastnetmon_mayflower.conf --daemonize
./fastnetmon --configuration_file=/etc/fastnetmon_hetzner.conf --daemonize
FastNetMon cli client expects stats file with default path /tmp/fastnetmon.dat so you need to set custom path with environment variable:
cli_stats_file_path=/tmp/fastnetmon_second_instance.dat ./fastnetmon_client