Q:

Prometheus Alertmanager HA config in config file

In the documentation I see you can provide flags to specify the high availability information: https://github.com/prometheus/alertmanager#high-availability
How do I specify these things in the config file instead of as CLI params? 

A:

These can only be specified on the command line. 
In general in Prometheus, a setting is either in the config or on the command line - never both.